Starting phenix.real_space_refine on Sun Jul 5 00:11:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mca_23755/07_2026/7mca_23755.map" } resolution = 3.6 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= 0.003 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 112 5.49 5 Mg 4 5.21 5 S 104 5.16 5 C 15509 2.51 5 N 4145 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24692 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 483} Chain breaks: 3 Chain: "B" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2096 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain breaks: 1 Chain: "C" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4830 Classifications: {'peptide': 584} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3572 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "E" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3702 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1369 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1018 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "H" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1032 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2999 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.82, per 1000 atoms: 0.20 Number of scatterers: 24692 At special positions: 0 Unit cell: (117.576, 138.276, 182.988, 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 104 16.00 P 112 15.00 Mg 4 11.99 O 4818 8.00 N 4145 7.00 C 15509 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 17 sheets defined 49.5% alpha, 4.8% beta 21 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.505A pdb=" N LYS A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 378 " --> pdb=" O PHE A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.702A pdb=" N ILE A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.900A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 397 " --> pdb=" O PHE A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.771A pdb=" N LYS A 409 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 410 " --> pdb=" O GLU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 455 through 468 removed outlier: 4.400A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Processing helix chain 'A' and resid 522 through 534 removed outlier: 4.325A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.668A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 699 removed outlier: 4.186A pdb=" N LYS A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 726 removed outlier: 3.653A pdb=" N ALA A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 5.476A pdb=" N LYS A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 798 through 816 removed outlier: 3.600A pdb=" N MET A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 836 removed outlier: 3.625A pdb=" N ILE A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 4.229A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 removed outlier: 3.746A pdb=" N LEU A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.732A pdb=" N MET B 265 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.703A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.564A pdb=" N GLN B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 removed outlier: 3.679A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.532A pdb=" N SER B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.641A pdb=" N TRP B 465 " --> pdb=" O PRO B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 removed outlier: 3.554A pdb=" N ASN B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 91 removed outlier: 3.954A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 156 removed outlier: 3.708A pdb=" N MET C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.628A pdb=" N ASN C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.564A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 230' Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.563A pdb=" N ILE C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 279 through 286 removed outlier: 3.547A pdb=" N LEU C 285 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.989A pdb=" N THR C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 removed outlier: 4.039A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 4.437A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 345 " --> pdb=" O ASN C 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 345' Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.522A pdb=" N LEU C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 370 Processing helix chain 'C' and resid 373 through 382 removed outlier: 4.117A pdb=" N ILE C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.262A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 removed outlier: 3.906A pdb=" N LEU C 396 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 397 " --> pdb=" O GLU C 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 393 through 397' Processing helix chain 'C' and resid 405 through 415 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 removed outlier: 3.749A pdb=" N TYR C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 4.040A pdb=" N LYS C 450 " --> pdb=" O LYS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.844A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.704A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.637A pdb=" N PHE C 544 " --> pdb=" O PHE C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 564 through 569 removed outlier: 3.929A pdb=" N GLU C 568 " --> pdb=" O THR C 564 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 564 through 569' Processing helix chain 'C' and resid 574 through 592 removed outlier: 4.221A pdb=" N ILE C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 4.032A pdb=" N LEU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.364A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 228 through 240 removed outlier: 4.190A pdb=" N VAL D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.826A pdb=" N SER D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.870A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 4.366A pdb=" N GLU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 removed outlier: 3.501A pdb=" N GLU D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 348 removed outlier: 3.744A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 343 - end of helix removed outlier: 3.679A pdb=" N SER D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.665A pdb=" N GLU D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.786A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.562A pdb=" N ALA D 487 " --> pdb=" O ALA D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.526A pdb=" N THR D 495 " --> pdb=" O PHE D 492 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D 496 " --> pdb=" O GLN D 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 492 through 496' Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.526A pdb=" N LEU D 501 " --> pdb=" O PRO D 498 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 498 through 502' Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.556A pdb=" N ARG D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.626A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.703A pdb=" N THR E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 69 through 87 removed outlier: 3.689A pdb=" N LEU E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.553A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.069A pdb=" N THR E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.698A pdb=" N ARG E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 229 through 247 removed outlier: 4.496A pdb=" N VAL E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.537A pdb=" N LEU E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 288 through 292 Processing helix chain 'E' and resid 325 through 339 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 removed outlier: 3.509A pdb=" N LEU E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.673A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.590A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 292 removed outlier: 3.583A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 306 removed outlier: 4.097A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 327 removed outlier: 4.260A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS F 321 " --> pdb=" O TRP F 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 325 " --> pdb=" O CYS F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 removed outlier: 3.517A pdb=" N ARG F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 337 " --> pdb=" O ASN F 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 332 through 337' Processing helix chain 'F' and resid 340 through 354 removed outlier: 3.569A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 371 removed outlier: 3.752A pdb=" N CYS F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS F 367 " --> pdb=" O ILE F 363 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.901A pdb=" N ILE F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 402 removed outlier: 4.510A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 402 " --> pdb=" O ILE F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 424 removed outlier: 4.270A pdb=" N ASN F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG F 424 " --> pdb=" O ILE F 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.578A pdb=" N MET I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 207 Processing helix chain 'I' and resid 238 through 245 Processing helix chain 'I' and resid 292 through 303 removed outlier: 3.778A pdb=" N MET I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 323 Processing helix chain 'I' and resid 330 through 346 removed outlier: 3.717A pdb=" N LEU I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP I 336 " --> pdb=" O ARG I 332 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 338 " --> pdb=" O LEU I 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG I 339 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY I 340 " --> pdb=" O ASP I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 349 No H-bonds generated for 'chain 'I' and resid 347 through 349' Processing helix chain 'I' and resid 389 through 399 removed outlier: 3.811A pdb=" N SER I 395 " --> pdb=" O ALA I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 410 removed outlier: 3.646A pdb=" N ARG I 406 " --> pdb=" O SER I 402 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 411 through 414 Processing helix chain 'I' and resid 415 through 423 removed outlier: 3.962A pdb=" N CYS I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 439 Processing helix chain 'I' and resid 454 through 468 removed outlier: 3.811A pdb=" N PHE I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR I 463 " --> pdb=" O LEU I 459 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE I 464 " --> pdb=" O GLU I 460 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 465 " --> pdb=" O ILE I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 502 removed outlier: 3.501A pdb=" N MET I 502 " --> pdb=" O PHE I 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 477 through 478 Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 514 removed outlier: 3.643A pdb=" N VAL A 562 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 651 Processing sheet with id=AA4, first strand: chain 'A' and resid 682 through 684 Processing sheet with id=AA5, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA6, first strand: chain 'B' and resid 475 through 477 removed outlier: 6.328A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 240 removed outlier: 6.299A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 127 through 131 Processing sheet with id=AA9, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.471A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.907A pdb=" N SER D 97 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.770A pdb=" N HIS E 58 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE E 131 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB6, first strand: chain 'I' and resid 105 through 106 removed outlier: 3.557A pdb=" N ILE I 106 " --> pdb=" O GLY I 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 170 through 171 removed outlier: 7.524A pdb=" N ILE I 170 " --> pdb=" O ASP I 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 475 through 476 removed outlier: 3.604A pdb=" N THR I 476 " --> pdb=" O VAL I 486 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL I 486 " --> pdb=" O THR I 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 764 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 9510 1.38 - 1.55: 15478 1.55 - 1.73: 218 1.73 - 1.90: 165 1.90 - 2.08: 4 Bond restraints: 25375 Sorted by residual: bond pdb=" C4 AGS D2001 " pdb=" C5 AGS D2001 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C5 AGS D2001 " pdb=" C6 AGS D2001 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" PG AGS D2001 " pdb=" S1G AGS D2001 " ideal model delta sigma weight residual 1.949 2.076 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C8 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 1.311 1.357 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.94e+01 ... (remaining 25370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 34189 3.12 - 6.24: 477 6.24 - 9.36: 53 9.36 - 12.48: 6 12.48 - 15.60: 2 Bond angle restraints: 34727 Sorted by residual: angle pdb=" C5 AGS D2001 " pdb=" C4 AGS D2001 " pdb=" N3 AGS D2001 " ideal model delta sigma weight residual 126.80 118.79 8.01 7.41e-01 1.82e+00 1.17e+02 angle pdb=" C4 AGS D2001 " pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 110.73 106.70 4.03 4.52e-01 4.89e+00 7.95e+01 angle pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " pdb=" C8 AGS D2001 " ideal model delta sigma weight residual 103.67 107.42 -3.75 4.26e-01 5.51e+00 7.74e+01 angle pdb=" N3 AGS D2001 " pdb=" C4 AGS D2001 " pdb=" N9 AGS D2001 " ideal model delta sigma weight residual 127.16 134.97 -7.81 1.06e+00 8.92e-01 5.44e+01 angle pdb=" C4 AGS D2001 " pdb=" N9 AGS D2001 " pdb=" C8 AGS D2001 " ideal model delta sigma weight residual 105.70 108.58 -2.88 4.55e-01 4.83e+00 4.01e+01 ... (remaining 34722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 14232 33.57 - 67.14: 880 67.14 - 100.72: 43 100.72 - 134.29: 1 134.29 - 167.86: 1 Dihedral angle restraints: 15157 sinusoidal: 6956 harmonic: 8201 Sorted by residual: dihedral pdb=" CA GLU I 235 " pdb=" C GLU I 235 " pdb=" N THR I 236 " pdb=" CA THR I 236 " ideal model delta harmonic sigma weight residual -180.00 -137.59 -42.41 0 5.00e+00 4.00e-02 7.19e+01 dihedral pdb=" CA PHE I 126 " pdb=" C PHE I 126 " pdb=" N GLN I 127 " pdb=" CA GLN I 127 " ideal model delta harmonic sigma weight residual 180.00 -143.87 -36.13 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA LEU I 282 " pdb=" C LEU I 282 " pdb=" N PRO I 283 " pdb=" CA PRO I 283 " ideal model delta harmonic sigma weight residual -180.00 -146.71 -33.29 0 5.00e+00 4.00e-02 4.43e+01 ... (remaining 15154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3288 0.078 - 0.155: 612 0.155 - 0.233: 49 0.233 - 0.310: 8 0.310 - 0.388: 3 Chirality restraints: 3960 Sorted by residual: chirality pdb=" CB ILE D 508 " pdb=" CA ILE D 508 " pdb=" CG1 ILE D 508 " pdb=" CG2 ILE D 508 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB ILE A 622 " pdb=" CA ILE A 622 " pdb=" CG1 ILE A 622 " pdb=" CG2 ILE A 622 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB ILE B 432 " pdb=" CA ILE B 432 " pdb=" CG1 ILE B 432 " pdb=" CG2 ILE B 432 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3957 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 214 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS I 214 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS I 214 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS I 215 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 454 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO E 455 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 455 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 455 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER I 395 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C SER I 395 " -0.051 2.00e-02 2.50e+03 pdb=" O SER I 395 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS I 396 " 0.017 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 13 1.82 - 2.59: 268 2.59 - 3.36: 29999 3.36 - 4.13: 59776 4.13 - 4.90: 108925 Nonbonded interactions: 198981 Sorted by model distance: nonbonded pdb=" O4 DT G 7 " pdb=" N1 DA H 79 " model vdw 1.053 2.496 nonbonded pdb=" N3 DT G 5 " pdb=" N1 DA H 81 " model vdw 1.099 3.200 nonbonded pdb=" O4 DT G 5 " pdb=" N6 DA H 81 " model vdw 1.161 3.120 nonbonded pdb=" O4 DT G 6 " pdb=" N1 DA H 80 " model vdw 1.375 2.496 nonbonded pdb=" O2 DT G 5 " pdb=" C2 DA H 81 " model vdw 1.508 3.340 ... (remaining 198976 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.070 Find NCS groups from input model: 0.260 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.008 0.417 25379 Z= 0.541 Angle : 0.998 15.601 34727 Z= 0.619 Chirality : 0.059 0.388 3960 Planarity : 0.006 0.076 4013 Dihedral : 19.349 167.859 9803 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 0.75 % Allowed : 10.87 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.13 (0.12), residues: 2718 helix: -3.47 (0.09), residues: 1379 sheet: -2.53 (0.33), residues: 197 loop : -3.33 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 267 TYR 0.031 0.003 TYR C 483 PHE 0.051 0.002 PHE I 126 TRP 0.014 0.002 TRP B 305 HIS 0.011 0.002 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.42 (25375) covalent geometry : angle 0.99832 / 0.62 (34727) hydrogen bonds : bond 0.17497 / 10.92 ( 813) hydrogen bonds : angle 8.09610 / 5.30 ( 2309) Misc. bond : bond 0.27355 / 15.43 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 495 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9136 (tp) cc_final: 0.8843 (tt) REVERT: B 262 THR cc_start: 0.8177 (m) cc_final: 0.7775 (t) REVERT: B 380 THR cc_start: 0.7608 (p) cc_final: 0.7290 (t) REVERT: C 37 LYS cc_start: 0.6776 (tptt) cc_final: 0.6492 (tptt) REVERT: C 100 ARG cc_start: 0.6778 (mmt180) cc_final: 0.6423 (mpt180) REVERT: C 186 SER cc_start: 0.7665 (p) cc_final: 0.7144 (t) REVERT: C 421 ASN cc_start: 0.7769 (t0) cc_final: 0.7510 (t0) REVERT: C 469 ASP cc_start: 0.7527 (t0) cc_final: 0.5899 (t0) REVERT: D 284 MET cc_start: 0.8296 (mtp) cc_final: 0.8044 (mtp) REVERT: D 454 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7937 (mttt) REVERT: E 297 ASP cc_start: 0.6726 (m-30) cc_final: 0.6084 (p0) REVERT: F 273 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8484 (pp) REVERT: I 87 GLN cc_start: 0.3942 (tm-30) cc_final: 0.3586 (mt0) REVERT: I 226 ASP cc_start: 0.5007 (m-30) cc_final: 0.4743 (m-30) REVERT: I 268 LYS cc_start: 0.3708 (tppt) cc_final: 0.3221 (tttt) REVERT: I 334 LEU cc_start: 0.8162 (tp) cc_final: 0.7708 (tp) REVERT: I 484 ARG cc_start: 0.5035 (mtt90) cc_final: 0.4755 (mtm110) outliers start: 19 outliers final: 5 residues processed: 512 average time/residue: 0.2027 time to fit residues: 155.8074 Evaluate side-chains 281 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 275 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 409 LYS Chi-restraints excluded: chain I residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 600 ASN A 771 GLN A 820 GLN B 256 ASN B 284 ASN B 291 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS B 478 HIS B 493 GLN C 67 HIS C 178 ASN C 241 ASN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN C 523 GLN C 536 ASN D 137 HIS D 255 ASN D 306 ASN D 370 ASN D 371 GLN D 409 ASN D 458 ASN E 32 ASN E 52 ASN E 82 GLN E 113 HIS E 139 GLN E 182 HIS E 193 ASN E 223 GLN E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN I 99 HIS I 193 ASN I 198 GLN I 213 HIS I 313 GLN I 439 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.162368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127570 restraints weight = 35736.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127025 restraints weight = 32990.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.128277 restraints weight = 30903.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128522 restraints weight = 21306.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128874 restraints weight = 19181.729| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25379 Z= 0.211 Angle : 0.714 12.242 34727 Z= 0.379 Chirality : 0.048 0.246 3960 Planarity : 0.005 0.063 4013 Dihedral : 19.630 165.799 4167 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.60 % Allowed : 15.75 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.14), residues: 2718 helix: -2.21 (0.12), residues: 1380 sheet: -2.45 (0.35), residues: 185 loop : -3.07 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 271 TYR 0.033 0.002 TYR I 291 PHE 0.048 0.002 PHE I 126 TRP 0.012 0.001 TRP F 378 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (25375) covalent geometry : angle 0.71443 / 0.38 (34727) hydrogen bonds : bond 0.05674 / 3.37 ( 813) hydrogen bonds : angle 5.02199 / 3.44 ( 2309) Misc. bond : bond 0.00919 / 0.48 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 316 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9270 (tp) cc_final: 0.8992 (tt) REVERT: A 566 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: B 262 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7697 (t) REVERT: B 380 THR cc_start: 0.7971 (p) cc_final: 0.7658 (t) REVERT: C 37 LYS cc_start: 0.6824 (tptt) cc_final: 0.6609 (tptt) REVERT: C 98 LYS cc_start: 0.6515 (tptp) cc_final: 0.5986 (mtmm) REVERT: C 100 ARG cc_start: 0.7189 (mmt180) cc_final: 0.6680 (ptp-170) REVERT: C 186 SER cc_start: 0.7687 (p) cc_final: 0.7481 (t) REVERT: C 241 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6955 (t0) REVERT: C 421 ASN cc_start: 0.7912 (t0) cc_final: 0.7662 (t0) REVERT: D 454 LYS cc_start: 0.8539 (ttpt) cc_final: 0.7921 (mttt) REVERT: D 471 GLU cc_start: 0.7493 (mp0) cc_final: 0.7002 (mp0) REVERT: D 512 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7214 (mt-10) REVERT: E 297 ASP cc_start: 0.6936 (m-30) cc_final: 0.6171 (p0) REVERT: E 320 GLN cc_start: 0.4441 (OUTLIER) cc_final: 0.4108 (pt0) REVERT: F 273 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8499 (pp) REVERT: I 268 LYS cc_start: 0.3655 (tppt) cc_final: 0.3142 (tptm) REVERT: I 334 LEU cc_start: 0.8046 (tp) cc_final: 0.7741 (tp) REVERT: I 418 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7255 (tt) REVERT: I 477 LYS cc_start: 0.8560 (mmtt) cc_final: 0.7947 (mtpt) outliers start: 66 outliers final: 33 residues processed: 363 average time/residue: 0.1634 time to fit residues: 94.7443 Evaluate side-chains 298 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 165 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN B 364 ASN B 493 GLN C 126 ASN C 178 ASN C 342 ASN C 430 ASN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 248 HIS E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122095 restraints weight = 36389.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120826 restraints weight = 32302.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122258 restraints weight = 33324.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122470 restraints weight = 21510.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122830 restraints weight = 19731.819| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 25379 Z= 0.314 Angle : 0.767 15.139 34727 Z= 0.400 Chirality : 0.050 0.250 3960 Planarity : 0.005 0.050 4013 Dihedral : 19.762 164.796 4161 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.94 % Allowed : 18.23 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.14), residues: 2718 helix: -1.87 (0.13), residues: 1371 sheet: -2.81 (0.34), residues: 186 loop : -3.05 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 888 TYR 0.025 0.002 TYR D 524 PHE 0.034 0.002 PHE C 102 TRP 0.014 0.002 TRP C 58 HIS 0.009 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.31 (25375) covalent geometry : angle 0.76696 / 0.40 (34727) hydrogen bonds : bond 0.05236 / 3.28 ( 813) hydrogen bonds : angle 4.99050 / 3.41 ( 2309) Misc. bond : bond 0.00394 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 283 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9347 (tp) cc_final: 0.9104 (tt) REVERT: A 566 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: A 722 MET cc_start: 0.8205 (tpp) cc_final: 0.7977 (mtp) REVERT: B 262 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7676 (t) REVERT: C 98 LYS cc_start: 0.6676 (tptp) cc_final: 0.6346 (ttmt) REVERT: C 100 ARG cc_start: 0.7421 (mmt180) cc_final: 0.6816 (ptp-170) REVERT: C 186 SER cc_start: 0.7970 (p) cc_final: 0.7685 (t) REVERT: C 421 ASN cc_start: 0.8019 (t0) cc_final: 0.7806 (t0) REVERT: D 113 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6953 (t0) REVERT: D 454 LYS cc_start: 0.8613 (ttpt) cc_final: 0.7944 (mttt) REVERT: D 471 GLU cc_start: 0.7706 (mp0) cc_final: 0.7288 (mp0) REVERT: D 512 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: D 514 ARG cc_start: 0.7717 (tpt170) cc_final: 0.7333 (ttt90) REVERT: E 171 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8699 (tt) REVERT: E 297 ASP cc_start: 0.7002 (m-30) cc_final: 0.6133 (p0) REVERT: F 273 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8497 (pp) REVERT: I 268 LYS cc_start: 0.3312 (tppt) cc_final: 0.2829 (tptm) REVERT: I 318 LYS cc_start: 0.7048 (mmtt) cc_final: 0.6489 (pptt) REVERT: I 418 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7146 (tt) outliers start: 100 outliers final: 63 residues processed: 360 average time/residue: 0.1560 time to fit residues: 89.7231 Evaluate side-chains 326 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5073 > 50: distance: 38 - 58: 13.585 distance: 42 - 66: 21.748 distance: 54 - 58: 11.840 distance: 58 - 59: 9.231 distance: 59 - 60: 34.709 distance: 59 - 62: 7.529 distance: 60 - 61: 9.258 distance: 60 - 66: 27.201 distance: 62 - 63: 16.788 distance: 63 - 64: 23.092 distance: 63 - 65: 26.393 distance: 66 - 67: 26.608 distance: 67 - 68: 11.766 distance: 67 - 70: 24.456 distance: 68 - 69: 9.933 distance: 68 - 72: 25.047 distance: 70 - 71: 21.369 distance: 72 - 73: 9.777 distance: 73 - 74: 10.625 distance: 73 - 76: 3.751 distance: 74 - 75: 16.261 distance: 74 - 86: 8.623 distance: 76 - 77: 8.556 distance: 77 - 78: 7.484 distance: 77 - 79: 6.508 distance: 78 - 80: 6.629 distance: 79 - 81: 4.150 distance: 79 - 82: 4.096 distance: 80 - 81: 4.430 distance: 84 - 85: 3.928 distance: 86 - 87: 6.679 distance: 87 - 88: 3.791 distance: 87 - 90: 12.569 distance: 88 - 89: 15.169 distance: 88 - 95: 9.105 distance: 90 - 91: 8.744 distance: 91 - 92: 8.990 distance: 92 - 93: 7.761 distance: 92 - 94: 7.015 distance: 95 - 96: 19.351 distance: 96 - 97: 6.043 distance: 96 - 99: 13.147 distance: 97 - 98: 20.419 distance: 97 - 104: 19.931 distance: 99 - 100: 16.612 distance: 100 - 101: 8.382 distance: 101 - 102: 7.133 distance: 101 - 103: 8.102 distance: 104 - 105: 46.022 distance: 105 - 106: 49.119 distance: 105 - 108: 42.781 distance: 106 - 107: 29.490 distance: 106 - 111: 18.258 distance: 108 - 109: 14.041 distance: 108 - 110: 10.892 distance: 111 - 112: 22.605 distance: 112 - 113: 19.221 distance: 112 - 115: 24.215 distance: 113 - 114: 16.853 distance: 113 - 119: 23.581 distance: 115 - 116: 15.129 distance: 116 - 117: 5.150 distance: 116 - 118: 36.001 distance: 119 - 120: 26.356 distance: 119 - 125: 18.811 distance: 120 - 121: 27.637 distance: 120 - 123: 22.622 distance: 121 - 122: 21.977 distance: 123 - 124: 18.758 distance: 124 - 125: 8.436 distance: 126 - 127: 10.781 distance: 127 - 128: 7.738 distance: 127 - 130: 16.240 distance: 128 - 129: 6.386 distance: 128 - 132: 6.031 distance: 130 - 131: 19.506 distance: 132 - 133: 23.387 distance: 133 - 134: 13.651 distance: 133 - 136: 7.283 distance: 134 - 135: 7.284 distance: 134 - 140: 26.733 distance: 136 - 137: 10.980 distance: 137 - 138: 22.531 distance: 137 - 139: 7.583