Starting phenix.real_space_refine on Sun Aug 24 17:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgr_22329/08_2025/7jgr_22329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgr_22329/08_2025/7jgr_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jgr_22329/08_2025/7jgr_22329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgr_22329/08_2025/7jgr_22329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jgr_22329/08_2025/7jgr_22329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgr_22329/08_2025/7jgr_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-2.0-5787/lib/python3.9/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: 4.99, per 1000 atoms: 0.23 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: 2.01 Conformation dependent library (CDL) restraints added in 877.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.76 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: 4.56 Time building geometry restraints manager: 2.60 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=" 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 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 ... (remaining 22228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 30175 4.24 - 8.48: 151 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: 11566 17.93 - 35.86: 1278 35.86 - 53.79: 492 53.79 - 71.72: 116 71.72 - 89.64: 26 Dihedral angle restraints: 13478 sinusoidal: 6058 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 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2834 0.063 - 0.126: 566 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 1.64e+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: 1.640 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.100 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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= 0.313 Angle : 0.952 21.197 30349 Z= 0.589 Chirality : 0.053 0.315 3503 Planarity : 0.006 0.087 3607 Dihedral : 17.946 89.644 8634 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 aren 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 covalent geometry : bond 0.00597 (22233) covalent geometry : angle 0.95169 (30349) hydrogen bonds : bond 0.15553 ( 1156) hydrogen bonds : angle 6.44275 ( 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 : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9470 (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: 0.8203 (pptt) REVERT: D 48 GLU cc_start: 0.8002 (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: 0.9177 (tt) REVERT: G 471 LYS cc_start: 0.9568 (tptt) cc_final: 0.9354 (tppt) REVERT: G 563 MET cc_start: 0.8728 (tmm) cc_final: 0.8435 (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: 0.8228 (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: 0.1944 time to fit residues: 168.1911 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 : 0.864 ------------------------------------------------------------------------------- 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: 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: 0.8980 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: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN B 498 ASN B 577 GLN C 194 ASN C 250 HIS 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 421 GLN E 127 ASN ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045304 restraints weight = 102750.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046834 restraints weight = 53506.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047855 restraints weight = 34142.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048546 restraints weight = 24707.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048998 restraints weight = 19632.858| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22233 Z= 0.180 Angle : 0.689 10.442 30349 Z= 0.361 Chirality : 0.042 0.243 3503 Planarity : 0.005 0.113 3607 Dihedral : 17.776 84.970 3665 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.03 % Allowed : 12.93 % Favored : 85.05 % 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 aren not related in a simple way. whole: -0.46 (0.16), residues: 2481 helix: -0.01 (0.12), residues: 1488 sheet: -2.44 (0.29), residues: 225 loop : 0.20 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 337 TYR 0.017 0.002 TYR C 72 PHE 0.026 0.002 PHE C 215 TRP 0.015 0.002 TRP E 276 HIS 0.012 0.001 HIS G 641 Details of bonding type rmsd covalent geometry : bond 0.00408 (22233) covalent geometry : angle 0.68886 (30349) hydrogen bonds : bond 0.04717 ( 1156) hydrogen bonds : angle 4.58067 ( 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: 45 poor density : 260 time to evaluate : 0.906 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: B 342 LYS cc_start: 0.9539 (tttt) cc_final: 0.9298 (tptp) REVERT: B 417 MET cc_start: 0.9474 (ttt) cc_final: 0.8686 (tmm) REVERT: B 553 MET cc_start: 0.9241 (ttp) cc_final: 0.8824 (ttt) REVERT: B 585 LYS cc_start: 0.9525 (mttt) cc_final: 0.9170 (tmtt) REVERT: C 72 TYR cc_start: 0.8493 (t80) cc_final: 0.8236 (t80) REVERT: C 145 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8754 (pp20) REVERT: C 280 ASP cc_start: 0.8719 (p0) cc_final: 0.8480 (p0) REVERT: C 281 LYS cc_start: 0.9672 (mttm) cc_final: 0.9429 (mtmm) REVERT: C 362 PHE cc_start: 0.9001 (t80) cc_final: 0.8713 (t80) REVERT: C 389 LEU cc_start: 0.9184 (mt) cc_final: 0.8773 (mt) REVERT: C 402 LEU cc_start: 0.9467 (mt) cc_final: 0.9067 (pp) REVERT: C 571 LEU cc_start: 0.9531 (mm) cc_final: 0.9314 (tp) REVERT: C 625 MET cc_start: 0.8751 (mtp) cc_final: 0.8308 (ttp) REVERT: C 699 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8537 (mt-10) REVERT: E 11 LEU cc_start: 0.9602 (mt) cc_final: 0.9394 (tt) REVERT: E 82 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8899 (mt-10) REVERT: E 94 ASP cc_start: 0.8359 (t70) cc_final: 0.7914 (t0) REVERT: E 289 GLN cc_start: 0.9322 (tp40) cc_final: 0.8556 (tp-100) REVERT: E 292 MET cc_start: 0.8560 (mpp) cc_final: 0.7160 (mpp) REVERT: E 337 HIS cc_start: 0.8222 (t-90) cc_final: 0.7805 (t-90) REVERT: F 232 MET cc_start: 0.9431 (tpp) cc_final: 0.8955 (tpt) REVERT: A 524 MET cc_start: 0.9454 (mmm) cc_final: 0.9068 (mmp) REVERT: A 536 MET cc_start: 0.8784 (tpp) cc_final: 0.7936 (tpp) REVERT: A 728 MET cc_start: 0.8342 (mmp) cc_final: 0.8112 (mmp) REVERT: A 788 ASP cc_start: 0.9278 (m-30) cc_final: 0.8761 (m-30) REVERT: A 832 MET cc_start: 0.9331 (mmt) cc_final: 0.8835 (mmm) REVERT: A 894 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8367 (mt-10) REVERT: G 327 CYS cc_start: 0.8351 (m) cc_final: 0.8039 (m) REVERT: G 333 VAL cc_start: 0.9013 (t) cc_final: 0.8772 (p) REVERT: G 370 MET cc_start: 0.8833 (tpp) cc_final: 0.8624 (mmt) REVERT: G 378 ILE cc_start: 0.9261 (tt) cc_final: 0.9034 (tp) REVERT: G 563 MET cc_start: 0.8716 (tmm) cc_final: 0.8495 (tmm) REVERT: G 565 CYS cc_start: 0.9174 (m) cc_final: 0.8848 (p) REVERT: G 588 TYR cc_start: 0.9147 (t80) cc_final: 0.8630 (t80) REVERT: G 610 ASP cc_start: 0.9255 (m-30) cc_final: 0.8956 (m-30) outliers start: 45 outliers final: 21 residues processed: 289 average time/residue: 0.1590 time to fit residues: 72.1712 Evaluate side-chains 220 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 393 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 666 GLN 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 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 882 CYS Chi-restraints excluded: chain A residue 919 VAL 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: chunk 168 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 366 GLN B 609 GLN C 368 GLN ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN A 749 GLN ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043301 restraints weight = 105962.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044751 restraints weight = 56365.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045729 restraints weight = 36438.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046384 restraints weight = 26735.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046793 restraints weight = 21507.498| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22233 Z= 0.200 Angle : 0.651 13.236 30349 Z= 0.338 Chirality : 0.041 0.388 3503 Planarity : 0.004 0.074 3607 Dihedral : 17.618 83.195 3661 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.57 % Allowed : 13.65 % Favored : 83.78 % 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 aren not related in a simple way. whole: 0.54 (0.17), residues: 2481 helix: 0.94 (0.13), residues: 1503 sheet: -2.02 (0.30), residues: 234 loop : 0.24 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 266 TYR 0.017 0.001 TYR B 356 PHE 0.027 0.002 PHE C 318 TRP 0.017 0.001 TRP E 276 HIS 0.009 0.001 HIS G 641 Details of bonding type rmsd covalent geometry : bond 0.00438 (22233) covalent geometry : angle 0.65051 (30349) hydrogen bonds : bond 0.04337 ( 1156) hydrogen bonds : angle 4.30190 ( 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 266 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.718 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: 0.9531 (tttt) cc_final: 0.9284 (tptp) REVERT: B 391 LYS cc_start: 0.9384 (tptt) cc_final: 0.8988 (tptt) REVERT: B 395 ASP cc_start: 0.9145 (m-30) cc_final: 0.8913 (m-30) REVERT: B 417 MET cc_start: 0.9228 (ttt) cc_final: 0.8590 (tmm) REVERT: B 420 GLU cc_start: 0.8384 (pp20) cc_final: 0.8184 (pp20) REVERT: B 585 LYS cc_start: 0.9530 (mttt) cc_final: 0.9202 (tmtt) REVERT: C 72 TYR cc_start: 0.8535 (t80) cc_final: 0.8220 (t80) REVERT: C 281 LYS cc_start: 0.9645 (mttm) cc_final: 0.9400 (mtmm) REVERT: C 306 TYR cc_start: 0.9288 (m-80) cc_final: 0.9015 (m-80) REVERT: C 362 PHE cc_start: 0.8989 (t80) cc_final: 0.8700 (t80) REVERT: C 389 LEU cc_start: 0.9215 (mt) cc_final: 0.8778 (mt) REVERT: C 402 LEU cc_start: 0.9491 (mt) cc_final: 0.9053 (pp) REVERT: C 446 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9192 (tp30) REVERT: C 454 LEU cc_start: 0.8945 (mt) cc_final: 0.8660 (tp) REVERT: C 666 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: C 699 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8546 (mt-10) REVERT: E 11 LEU cc_start: 0.9603 (mt) cc_final: 0.9366 (tt) REVERT: E 82 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8817 (mt-10) REVERT: E 94 ASP cc_start: 0.8437 (t70) cc_final: 0.7988 (t0) REVERT: E 254 CYS cc_start: 0.8737 (m) cc_final: 0.8088 (t) REVERT: E 292 MET cc_start: 0.8649 (mpp) cc_final: 0.8225 (mpp) REVERT: E 395 GLU cc_start: 0.9170 (tp30) cc_final: 0.8709 (mm-30) REVERT: F 232 MET cc_start: 0.9430 (tpp) cc_final: 0.8991 (tpt) REVERT: F 233 LEU cc_start: 0.9293 (pp) cc_final: 0.9045 (pp) REVERT: A 524 MET cc_start: 0.9458 (mmm) cc_final: 0.8946 (mmp) REVERT: A 536 MET cc_start: 0.8993 (tpp) cc_final: 0.8444 (tpp) REVERT: A 728 MET cc_start: 0.8460 (mmp) cc_final: 0.8123 (mmm) REVERT: A 788 ASP cc_start: 0.9186 (m-30) cc_final: 0.8712 (m-30) REVERT: A 832 MET cc_start: 0.9387 (mmt) cc_final: 0.8933 (mmm) REVERT: A 894 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8424 (mt-10) REVERT: G 327 CYS cc_start: 0.8540 (m) cc_final: 0.8138 (m) REVERT: G 333 VAL cc_start: 0.9108 (t) cc_final: 0.8869 (p) REVERT: G 370 MET cc_start: 0.8914 (tpp) cc_final: 0.8536 (mmt) REVERT: G 376 ASP cc_start: 0.8485 (t70) cc_final: 0.8227 (t0) REVERT: G 378 ILE cc_start: 0.9352 (tt) cc_final: 0.9122 (tp) REVERT: G 563 MET cc_start: 0.8740 (tmm) cc_final: 0.8525 (tmm) REVERT: G 565 CYS cc_start: 0.9188 (m) cc_final: 0.8855 (p) REVERT: G 588 TYR cc_start: 0.9081 (t80) cc_final: 0.8755 (t80) REVERT: G 610 ASP cc_start: 0.9272 (m-30) cc_final: 0.8942 (m-30) outliers start: 57 outliers final: 27 residues processed: 253 average time/residue: 0.1450 time to fit residues: 59.0926 Evaluate side-chains 211 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 666 GLN 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 217 CYS Chi-restraints excluded: chain E residue 385 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 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 338 LYS Chi-restraints excluded: chain G residue 352 THR 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: chunk 172 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 157 optimal weight: 0.2980 chunk 235 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 609 GLN C 368 GLN C 666 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.043941 restraints weight = 104698.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.045349 restraints weight = 55610.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046300 restraints weight = 36089.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046951 restraints weight = 26547.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047367 restraints weight = 21374.850| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22233 Z= 0.180 Angle : 0.611 9.823 30349 Z= 0.319 Chirality : 0.041 0.359 3503 Planarity : 0.004 0.058 3607 Dihedral : 17.495 84.011 3661 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 15.68 % Favored : 81.85 % 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 aren not related in a simple way. whole: 0.87 (0.17), residues: 2481 helix: 1.33 (0.14), residues: 1511 sheet: -1.97 (0.29), residues: 240 loop : 0.11 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 575 TYR 0.016 0.001 TYR B 356 PHE 0.020 0.001 PHE C 318 TRP 0.009 0.001 TRP C 191 HIS 0.009 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00397 (22233) covalent geometry : angle 0.61070 (30349) hydrogen bonds : bond 0.03915 ( 1156) hydrogen bonds : angle 4.15521 ( 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 249 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.855 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: 0.9505 (tttt) cc_final: 0.9266 (tptp) REVERT: B 391 LYS cc_start: 0.9365 (tptt) cc_final: 0.8999 (tptt) REVERT: B 395 ASP cc_start: 0.9126 (m-30) cc_final: 0.8924 (m-30) REVERT: B 417 MET cc_start: 0.9282 (ttt) cc_final: 0.8739 (tmm) REVERT: B 553 MET cc_start: 0.9182 (ttp) cc_final: 0.8789 (ttt) REVERT: B 585 LYS cc_start: 0.9514 (mttt) cc_final: 0.9263 (tmtt) REVERT: C 72 TYR cc_start: 0.8474 (t80) cc_final: 0.8176 (t80) REVERT: C 145 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8837 (pp20) REVERT: C 246 MET cc_start: 0.8697 (mpp) cc_final: 0.8411 (mmm) REVERT: C 281 LYS cc_start: 0.9606 (mttm) cc_final: 0.9376 (mtmm) REVERT: C 306 TYR cc_start: 0.9272 (m-80) cc_final: 0.9038 (m-80) REVERT: C 362 PHE cc_start: 0.9025 (t80) cc_final: 0.8696 (t80) REVERT: C 389 LEU cc_start: 0.9258 (mt) cc_final: 0.8844 (mt) REVERT: C 402 LEU cc_start: 0.9472 (mt) cc_final: 0.9057 (pp) REVERT: C 446 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9229 (tp30) REVERT: C 454 LEU cc_start: 0.8963 (mt) cc_final: 0.8727 (tp) REVERT: C 571 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9364 (tp) REVERT: C 699 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8547 (mt-10) REVERT: D 205 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9337 (mm) REVERT: E 11 LEU cc_start: 0.9561 (mt) cc_final: 0.9335 (tt) REVERT: E 82 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8779 (mt-10) REVERT: E 94 ASP cc_start: 0.8348 (t70) cc_final: 0.7870 (t0) REVERT: E 254 CYS cc_start: 0.8792 (m) cc_final: 0.8193 (t) REVERT: E 292 MET cc_start: 0.8716 (mpp) cc_final: 0.8287 (mpp) REVERT: E 395 GLU cc_start: 0.9120 (tp30) cc_final: 0.8685 (mm-30) REVERT: E 425 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8810 (tp) REVERT: F 232 MET cc_start: 0.9392 (tpp) cc_final: 0.9022 (tpt) REVERT: A 524 MET cc_start: 0.9433 (mmm) cc_final: 0.8888 (mmp) REVERT: A 536 MET cc_start: 0.8916 (tpp) cc_final: 0.8400 (tpp) REVERT: A 728 MET cc_start: 0.8461 (mmp) cc_final: 0.8158 (mmm) REVERT: A 788 ASP cc_start: 0.9128 (m-30) cc_final: 0.8654 (m-30) REVERT: A 832 MET cc_start: 0.9341 (mmt) cc_final: 0.8946 (mmm) REVERT: G 327 CYS cc_start: 0.8403 (m) cc_final: 0.8019 (m) REVERT: G 333 VAL cc_start: 0.9180 (t) cc_final: 0.8947 (p) REVERT: G 370 MET cc_start: 0.8900 (tpp) cc_final: 0.8521 (mmt) REVERT: G 378 ILE cc_start: 0.9372 (tt) cc_final: 0.9131 (tp) REVERT: G 565 CYS cc_start: 0.9128 (m) cc_final: 0.8829 (p) REVERT: G 588 TYR cc_start: 0.9060 (t80) cc_final: 0.8773 (t80) REVERT: G 610 ASP cc_start: 0.9263 (m-30) cc_final: 0.8944 (m-30) outliers start: 55 outliers final: 35 residues processed: 235 average time/residue: 0.1384 time to fit residues: 52.7903 Evaluate side-chains 208 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 147 LEU 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 645 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 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 80 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 425 ILE 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 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 446 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 657 THR Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 21 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 0.0570 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN B 410 ASN C 368 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043750 restraints weight = 104689.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045198 restraints weight = 54981.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046180 restraints weight = 35306.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046835 restraints weight = 25734.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047286 restraints weight = 20589.515| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22233 Z= 0.136 Angle : 0.583 11.624 30349 Z= 0.300 Chirality : 0.040 0.446 3503 Planarity : 0.004 0.053 3607 Dihedral : 17.326 79.976 3661 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.12 % Allowed : 16.53 % Favored : 81.35 % 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 aren not related in a simple way. whole: 1.14 (0.17), residues: 2481 helix: 1.57 (0.14), residues: 1506 sheet: -1.72 (0.30), residues: 240 loop : 0.12 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 575 TYR 0.017 0.001 TYR G 324 PHE 0.018 0.001 PHE C 318 TRP 0.009 0.001 TRP E 276 HIS 0.007 0.001 HIS G 641 Details of bonding type rmsd covalent geometry : bond 0.00300 (22233) covalent geometry : angle 0.58334 (30349) hydrogen bonds : bond 0.03582 ( 1156) hydrogen bonds : angle 3.99133 ( 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 247 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.9514 (tttt) cc_final: 0.9275 (tptp) REVERT: B 391 LYS cc_start: 0.9384 (tptt) cc_final: 0.9009 (tptt) REVERT: B 395 ASP cc_start: 0.9180 (m-30) cc_final: 0.8905 (m-30) REVERT: B 417 MET cc_start: 0.9295 (ttt) cc_final: 0.8960 (tmm) REVERT: B 540 TYR cc_start: 0.8688 (t80) cc_final: 0.8455 (t80) REVERT: B 585 LYS cc_start: 0.9509 (mttt) cc_final: 0.9210 (tmtt) REVERT: C 1 MET cc_start: 0.7296 (ttm) cc_final: 0.6992 (ttt) REVERT: C 145 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8898 (pp20) REVERT: C 246 MET cc_start: 0.8735 (mpp) cc_final: 0.8375 (mmm) REVERT: C 281 LYS cc_start: 0.9587 (mttm) cc_final: 0.9340 (mtmm) REVERT: C 362 PHE cc_start: 0.9009 (t80) cc_final: 0.8609 (t80) REVERT: C 389 LEU cc_start: 0.9241 (mt) cc_final: 0.8825 (mt) REVERT: C 402 LEU cc_start: 0.9460 (mt) cc_final: 0.9052 (pp) REVERT: C 426 ARG cc_start: 0.8878 (mmt90) cc_final: 0.8642 (mmt90) REVERT: C 446 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9245 (tp30) REVERT: C 454 LEU cc_start: 0.8929 (mt) cc_final: 0.8719 (tp) REVERT: C 699 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8534 (mp0) REVERT: E 11 LEU cc_start: 0.9581 (mt) cc_final: 0.9313 (tt) REVERT: E 82 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8805 (mt-10) REVERT: E 94 ASP cc_start: 0.8398 (t70) cc_final: 0.7916 (t0) REVERT: E 254 CYS cc_start: 0.8753 (m) cc_final: 0.8180 (t) REVERT: E 292 MET cc_start: 0.8719 (mpp) cc_final: 0.8201 (mpp) REVERT: E 395 GLU cc_start: 0.9115 (tp30) cc_final: 0.8664 (mm-30) REVERT: F 232 MET cc_start: 0.9411 (tpp) cc_final: 0.9091 (tpt) REVERT: A 524 MET cc_start: 0.9446 (mmm) cc_final: 0.8885 (mmp) REVERT: A 536 MET cc_start: 0.8982 (tpp) cc_final: 0.8345 (tpp) REVERT: A 728 MET cc_start: 0.8496 (mmp) cc_final: 0.8186 (mmm) REVERT: A 788 ASP cc_start: 0.9162 (m-30) cc_final: 0.8695 (m-30) REVERT: A 805 VAL cc_start: 0.8874 (t) cc_final: 0.8514 (t) REVERT: A 832 MET cc_start: 0.9380 (mmt) cc_final: 0.8946 (mmm) REVERT: G 327 CYS cc_start: 0.8391 (m) cc_final: 0.7954 (m) REVERT: G 333 VAL cc_start: 0.9210 (t) cc_final: 0.8972 (p) REVERT: G 376 ASP cc_start: 0.8176 (t0) cc_final: 0.7829 (t0) REVERT: G 378 ILE cc_start: 0.9335 (tt) cc_final: 0.9077 (tp) REVERT: G 563 MET cc_start: 0.8718 (tmm) cc_final: 0.8470 (tmm) REVERT: G 565 CYS cc_start: 0.9200 (m) cc_final: 0.8891 (p) REVERT: G 588 TYR cc_start: 0.9025 (t80) cc_final: 0.8735 (t80) REVERT: G 594 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8924 (mtmt) REVERT: G 610 ASP cc_start: 0.9272 (m-30) cc_final: 0.8946 (m-30) outliers start: 47 outliers final: 33 residues processed: 234 average time/residue: 0.1332 time to fit residues: 50.6097 Evaluate side-chains 210 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 645 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 351 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 LEU 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 329 LEU Chi-restraints excluded: chain A residue 519 THR 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 338 LYS 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 594 LYS Chi-restraints excluded: chain G residue 657 THR Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 66 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 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 = 0.3228 r_free = 0.3228 target = 0.057300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.044510 restraints weight = 106332.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045923 restraints weight = 55684.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046872 restraints weight = 35585.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047516 restraints weight = 25838.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047917 restraints weight = 20637.421| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22233 Z= 0.160 Angle : 0.586 10.789 30349 Z= 0.304 Chirality : 0.040 0.328 3503 Planarity : 0.004 0.047 3607 Dihedral : 17.266 79.184 3661 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.61 % Allowed : 17.07 % Favored : 80.32 % 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 aren not related in a simple way. whole: 1.32 (0.17), residues: 2481 helix: 1.70 (0.14), residues: 1519 sheet: -1.56 (0.30), residues: 240 loop : 0.14 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 575 TYR 0.015 0.001 TYR A 579 PHE 0.013 0.001 PHE C 318 TRP 0.012 0.001 TRP B 343 HIS 0.007 0.001 HIS G 641 Details of bonding type rmsd covalent geometry : bond 0.00356 (22233) covalent geometry : angle 0.58616 (30349) hydrogen bonds : bond 0.03640 ( 1156) hydrogen bonds : angle 3.97997 ( 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 237 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.879 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 395 ASP cc_start: 0.9172 (m-30) cc_final: 0.8853 (m-30) REVERT: B 417 MET cc_start: 0.9275 (ttt) cc_final: 0.8956 (tmm) REVERT: B 585 LYS cc_start: 0.9502 (mttt) cc_final: 0.9202 (tmtt) REVERT: B 588 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8313 (mtmm) REVERT: C 145 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8891 (pp20) REVERT: C 246 MET cc_start: 0.8687 (mpp) cc_final: 0.8411 (mmm) REVERT: C 362 PHE cc_start: 0.9022 (t80) cc_final: 0.8645 (t80) REVERT: C 389 LEU cc_start: 0.9276 (mt) cc_final: 0.8855 (mt) REVERT: C 402 LEU cc_start: 0.9446 (mt) cc_final: 0.9042 (pp) REVERT: C 446 GLU cc_start: 0.9524 (mt-10) cc_final: 0.9219 (tp30) REVERT: C 451 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8661 (pp) REVERT: C 699 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8655 (mp0) REVERT: D 239 TYR cc_start: 0.8457 (t80) cc_final: 0.8251 (t80) REVERT: E 11 LEU cc_start: 0.9559 (mt) cc_final: 0.9287 (tt) REVERT: E 82 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 94 ASP cc_start: 0.8353 (t70) cc_final: 0.7864 (t0) REVERT: E 254 CYS cc_start: 0.8758 (m) cc_final: 0.8209 (t) REVERT: E 292 MET cc_start: 0.8703 (mpp) cc_final: 0.8178 (mpp) REVERT: F 232 MET cc_start: 0.9427 (tpp) cc_final: 0.9127 (tpt) REVERT: A 524 MET cc_start: 0.9443 (mmm) cc_final: 0.8861 (mmp) REVERT: A 536 MET cc_start: 0.8973 (tpp) cc_final: 0.8363 (tpp) REVERT: A 728 MET cc_start: 0.8483 (mmp) cc_final: 0.8176 (mmm) REVERT: A 788 ASP cc_start: 0.9151 (m-30) cc_final: 0.8701 (m-30) REVERT: A 805 VAL cc_start: 0.8909 (t) cc_final: 0.8560 (t) REVERT: A 832 MET cc_start: 0.9377 (mmt) cc_final: 0.8949 (mmm) REVERT: G 327 CYS cc_start: 0.8373 (m) cc_final: 0.7931 (m) REVERT: G 333 VAL cc_start: 0.9208 (t) cc_final: 0.8978 (p) REVERT: G 370 MET cc_start: 0.8862 (tpp) cc_final: 0.8452 (mmt) REVERT: G 376 ASP cc_start: 0.8116 (t0) cc_final: 0.7615 (t0) REVERT: G 378 ILE cc_start: 0.9376 (tt) cc_final: 0.9110 (tp) REVERT: G 563 MET cc_start: 0.8695 (tmm) cc_final: 0.8442 (tmm) REVERT: G 565 CYS cc_start: 0.9159 (m) cc_final: 0.8875 (p) REVERT: G 581 MET cc_start: 0.9134 (mmm) cc_final: 0.8615 (tpp) REVERT: G 610 ASP cc_start: 0.9251 (m-30) cc_final: 0.8946 (m-30) outliers start: 58 outliers final: 42 residues processed: 224 average time/residue: 0.1484 time to fit residues: 54.3854 Evaluate side-chains 209 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 574 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 79 LEU 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 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 268 THR 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 645 LEU Chi-restraints excluded: chain C residue 652 HIS 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 324 MET 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 328 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain A residue 519 THR 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 882 CYS 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 576 ASN 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: chunk 115 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 HIS E 150 ASN E 414 ASN G 576 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.043513 restraints weight = 106041.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.044947 restraints weight = 55645.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045900 restraints weight = 35719.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046528 restraints weight = 26073.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.046990 restraints weight = 20931.143| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22233 Z= 0.137 Angle : 0.588 14.231 30349 Z= 0.301 Chirality : 0.040 0.324 3503 Planarity : 0.003 0.046 3607 Dihedral : 17.234 82.239 3661 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.57 % Allowed : 17.39 % Favored : 80.05 % 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 aren not related in a simple way. whole: 1.37 (0.17), residues: 2481 helix: 1.76 (0.14), residues: 1509 sheet: -1.40 (0.30), residues: 250 loop : 0.09 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 575 TYR 0.017 0.001 TYR C 72 PHE 0.014 0.001 PHE C 318 TRP 0.011 0.001 TRP E 276 HIS 0.006 0.001 HIS G 641 Details of bonding type rmsd covalent geometry : bond 0.00309 (22233) covalent geometry : angle 0.58846 (30349) hydrogen bonds : bond 0.03517 ( 1156) hydrogen bonds : angle 3.95209 ( 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 235 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.902 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 395 ASP cc_start: 0.9176 (m-30) cc_final: 0.8835 (m-30) REVERT: B 417 MET cc_start: 0.9302 (ttt) cc_final: 0.8963 (tmm) REVERT: B 585 LYS cc_start: 0.9501 (mttt) cc_final: 0.9206 (tmtt) REVERT: B 588 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8343 (mtmm) REVERT: C 145 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8876 (pp20) REVERT: C 246 MET cc_start: 0.8690 (mpp) cc_final: 0.8418 (mmm) REVERT: C 306 TYR cc_start: 0.9261 (m-80) cc_final: 0.9010 (m-80) REVERT: C 362 PHE cc_start: 0.9036 (t80) cc_final: 0.8652 (t80) REVERT: C 389 LEU cc_start: 0.9277 (mt) cc_final: 0.8864 (mt) REVERT: C 402 LEU cc_start: 0.9440 (mt) cc_final: 0.9044 (pp) REVERT: C 443 GLU cc_start: 0.9363 (mp0) cc_final: 0.9107 (mp0) REVERT: C 446 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9271 (tp30) REVERT: C 451 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8645 (pp) REVERT: C 699 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8628 (mp0) REVERT: D 239 TYR cc_start: 0.8506 (t80) cc_final: 0.8302 (t80) REVERT: E 11 LEU cc_start: 0.9572 (mt) cc_final: 0.9286 (tt) REVERT: E 82 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8797 (mt-10) REVERT: E 94 ASP cc_start: 0.8369 (t70) cc_final: 0.7873 (t0) REVERT: E 254 CYS cc_start: 0.8745 (m) cc_final: 0.8203 (t) REVERT: E 292 MET cc_start: 0.8694 (mpp) cc_final: 0.8143 (mpp) REVERT: E 440 PHE cc_start: 0.8851 (t80) cc_final: 0.8515 (t80) REVERT: F 232 MET cc_start: 0.9445 (tpp) cc_final: 0.9148 (tpt) REVERT: A 524 MET cc_start: 0.9437 (mmm) cc_final: 0.8856 (mmp) REVERT: A 536 MET cc_start: 0.8988 (tpp) cc_final: 0.8353 (tpp) REVERT: A 728 MET cc_start: 0.8486 (mmp) cc_final: 0.8172 (mmm) REVERT: A 788 ASP cc_start: 0.9123 (m-30) cc_final: 0.8684 (m-30) REVERT: A 805 VAL cc_start: 0.8887 (t) cc_final: 0.8537 (t) REVERT: A 832 MET cc_start: 0.9365 (mmt) cc_final: 0.8957 (mmm) REVERT: G 327 CYS cc_start: 0.8379 (m) cc_final: 0.7923 (m) REVERT: G 370 MET cc_start: 0.8843 (tpp) cc_final: 0.8409 (mmt) REVERT: G 376 ASP cc_start: 0.8116 (t0) cc_final: 0.7602 (t0) REVERT: G 378 ILE cc_start: 0.9367 (tt) cc_final: 0.9088 (tp) REVERT: G 563 MET cc_start: 0.8700 (tmm) cc_final: 0.8437 (tmm) REVERT: G 565 CYS cc_start: 0.9160 (m) cc_final: 0.8910 (p) REVERT: G 581 MET cc_start: 0.9128 (mmm) cc_final: 0.8707 (tpp) REVERT: G 610 ASP cc_start: 0.9260 (m-30) cc_final: 0.8961 (m-30) outliers start: 57 outliers final: 41 residues processed: 218 average time/residue: 0.1491 time to fit residues: 53.1838 Evaluate side-chains 218 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 574 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 268 THR 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 645 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 1 MET 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 329 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain A residue 519 THR 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0925 > 50: distance: 69 - 73: 33.106 distance: 73 - 74: 4.887 distance: 75 - 76: 40.566 distance: 77 - 78: 56.834 distance: 80 - 81: 41.416 distance: 80 - 83: 56.660 distance: 81 - 82: 39.246 distance: 81 - 88: 40.754 distance: 83 - 84: 40.697 distance: 84 - 85: 56.085 distance: 88 - 89: 39.450 distance: 89 - 90: 41.586 distance: 89 - 92: 8.894 distance: 90 - 91: 57.126 distance: 90 - 95: 14.259 distance: 92 - 94: 66.520 distance: 95 - 96: 16.873 distance: 96 - 97: 42.037 distance: 96 - 99: 16.784 distance: 97 - 98: 15.212 distance: 97 - 107: 47.294 distance: 99 - 100: 44.859 distance: 100 - 101: 41.667 distance: 101 - 103: 47.458 distance: 102 - 104: 14.552 distance: 103 - 105: 54.738 distance: 104 - 105: 26.704 distance: 105 - 106: 56.603 distance: 107 - 108: 40.772 distance: 107 - 113: 56.506 distance: 108 - 109: 38.504 distance: 108 - 111: 39.281 distance: 109 - 114: 33.068 distance: 111 - 112: 38.597 distance: 112 - 113: 38.734 distance: 114 - 115: 51.760 distance: 115 - 116: 25.021 distance: 115 - 118: 24.475 distance: 116 - 117: 16.492 distance: 116 - 120: 20.052 distance: 118 - 119: 26.586 distance: 120 - 121: 41.664 distance: 121 - 122: 27.388 distance: 121 - 124: 11.701 distance: 122 - 123: 12.682 distance: 122 - 125: 23.162 distance: 123 - 276: 33.976 distance: 125 - 126: 21.816 distance: 126 - 127: 39.792 distance: 126 - 129: 40.090 distance: 127 - 133: 29.987 distance: 129 - 131: 38.854 distance: 130 - 132: 39.649 distance: 133 - 134: 8.195 distance: 133 - 279: 18.407 distance: 134 - 135: 39.970 distance: 134 - 137: 6.378 distance: 135 - 145: 38.729 distance: 136 - 289: 32.329 distance: 137 - 138: 21.180 distance: 138 - 139: 40.097 distance: 138 - 140: 31.061 distance: 139 - 141: 20.876 distance: 140 - 142: 28.903 distance: 141 - 143: 21.876 distance: 145 - 146: 30.741 distance: 146 - 147: 41.435 distance: 146 - 149: 34.849 distance: 147 - 148: 10.867 distance: 147 - 153: 30.403 distance: 149 - 150: 23.020 distance: 150 - 152: 55.622