Starting phenix.real_space_refine on Sun Aug 24 09:31:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uw9_20920/08_2025/6uw9_20920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uw9_20920/08_2025/6uw9_20920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uw9_20920/08_2025/6uw9_20920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uw9_20920/08_2025/6uw9_20920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uw9_20920/08_2025/6uw9_20920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uw9_20920/08_2025/6uw9_20920.map" } resolution = 4.33 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= 0.004 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12340 2.51 5 N 3136 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18924 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4731 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 571} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Restraints were copied for chains: B, C, D Time building chain proxies: 3.65, per 1000 atoms: 0.19 Number of scatterers: 18924 At special positions: 0 Unit cell: (159.5, 159.5, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3336 8.00 N 3136 7.00 C 12340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 693.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 67.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 4.008A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.621A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 569 through 586 removed outlier: 4.360A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.883A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 706 removed outlier: 3.605A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.438A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.537A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 335 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 removed outlier: 4.008A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.904A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.883A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.166A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.622A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 567' Processing helix chain 'B' and resid 569 through 586 removed outlier: 4.361A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 706 removed outlier: 3.606A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.611A pdb=" N LEU C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.591A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C 335 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 4.007A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 501 removed outlier: 4.236A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.622A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 563 through 567' Processing helix chain 'C' and resid 569 through 586 removed outlier: 4.361A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 679 removed outlier: 3.704A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 706 removed outlier: 3.606A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.935A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 335 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 removed outlier: 4.007A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 431 " --> pdb=" O THR D 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.621A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 563 through 567' Processing helix chain 'D' and resid 569 through 586 removed outlier: 4.360A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 706 removed outlier: 3.605A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5464 1.34 - 1.46: 3429 1.46 - 1.57: 10235 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 19320 Sorted by residual: bond pdb=" C PRO B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.71e+01 bond pdb=" C PRO D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.70e+01 bond pdb=" C PRO C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.70e+01 bond pdb=" C PRO A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.332 1.220 0.112 1.29e-02 6.01e+03 7.59e+01 bond pdb=" C GLU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.331 1.386 -0.054 7.90e-03 1.60e+04 4.75e+01 ... (remaining 19315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 25675 3.29 - 6.59: 341 6.59 - 9.88: 64 9.88 - 13.17: 24 13.17 - 16.47: 16 Bond angle restraints: 26120 Sorted by residual: angle pdb=" CA PRO A 424 " pdb=" C PRO A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 118.81 103.11 15.70 1.61e+00 3.86e-01 9.51e+01 angle pdb=" CA PRO C 424 " pdb=" C PRO C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 118.81 103.15 15.66 1.61e+00 3.86e-01 9.46e+01 angle pdb=" CA PRO B 424 " pdb=" C PRO B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 118.81 103.17 15.64 1.61e+00 3.86e-01 9.44e+01 angle pdb=" CA PRO D 424 " pdb=" C PRO D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 118.81 103.17 15.64 1.61e+00 3.86e-01 9.44e+01 angle pdb=" C PRO A 424 " pdb=" N LEU A 425 " pdb=" CA LEU A 425 " ideal model delta sigma weight residual 122.60 106.13 16.47 1.88e+00 2.83e-01 7.67e+01 ... (remaining 26115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 9869 16.86 - 33.72: 1254 33.72 - 50.59: 277 50.59 - 67.45: 28 67.45 - 84.31: 16 Dihedral angle restraints: 11444 sinusoidal: 4600 harmonic: 6844 Sorted by residual: dihedral pdb=" CA ILE A 199 " pdb=" C ILE A 199 " pdb=" N LEU A 200 " pdb=" CA LEU A 200 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N LEU B 200 " pdb=" CA LEU B 200 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE C 199 " pdb=" C ILE C 199 " pdb=" N LEU C 200 " pdb=" CA LEU C 200 " ideal model delta harmonic sigma weight residual 180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2332 0.064 - 0.127: 528 0.127 - 0.191: 106 0.191 - 0.254: 26 0.254 - 0.318: 8 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA ASP B 586 " pdb=" N ASP B 586 " pdb=" C ASP B 586 " pdb=" CB ASP B 586 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA ASP A 586 " pdb=" N ASP A 586 " pdb=" C ASP A 586 " pdb=" CB ASP A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ASP C 586 " pdb=" N ASP C 586 " pdb=" C ASP C 586 " pdb=" CB ASP C 586 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2997 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 343 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 344 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 344 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO D 344 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.044 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 152 2.53 - 3.12: 12859 3.12 - 3.71: 29738 3.71 - 4.31: 37668 4.31 - 4.90: 62242 Nonbonded interactions: 142659 Sorted by model distance: nonbonded pdb=" SD MET A 431 " pdb=" NH1 ARG A 716 " model vdw 1.932 3.480 nonbonded pdb=" SD MET D 431 " pdb=" NH1 ARG D 716 " model vdw 1.933 3.480 nonbonded pdb=" SD MET C 431 " pdb=" NH1 ARG C 716 " model vdw 1.933 3.480 nonbonded pdb=" SD MET B 431 " pdb=" NH1 ARG B 716 " model vdw 1.933 3.480 nonbonded pdb=" SD MET D 431 " pdb=" CZ ARG D 716 " model vdw 1.973 3.630 ... (remaining 142654 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.390 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.005 0.113 19320 Z= 0.298 Angle : 1.144 16.467 26120 Z= 0.630 Chirality : 0.060 0.318 3000 Planarity : 0.007 0.081 3236 Dihedral : 15.426 84.310 6996 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.20 % Allowed : 11.22 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -4.94 (0.13), residues: 2288 helix: -3.02 (0.09), residues: 1424 sheet: -1.63 (0.86), residues: 40 loop : -3.58 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.015 0.002 TYR B 451 PHE 0.034 0.002 PHE D 656 TRP 0.012 0.001 TRP D 380 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00541 (19320) covalent geometry : angle 1.14426 (26120) hydrogen bonds : bond 0.16155 ( 996) hydrogen bonds : angle 6.92352 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 532 time to evaluate : 0.459 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: A 205 ASN cc_start: 0.8780 (m-40) cc_final: 0.8363 (p0) REVERT: A 268 LEU cc_start: 0.9407 (tp) cc_final: 0.9162 (tp) REVERT: A 366 LYS cc_start: 0.8790 (mppt) cc_final: 0.8357 (mmmt) REVERT: A 562 MET cc_start: 0.8934 (tpp) cc_final: 0.8636 (tpp) REVERT: A 592 PHE cc_start: 0.8665 (t80) cc_final: 0.8415 (t80) REVERT: A 595 ILE cc_start: 0.9398 (mm) cc_final: 0.9090 (tp) REVERT: A 672 MET cc_start: 0.9048 (tmm) cc_final: 0.8755 (tmm) REVERT: B 188 ARG cc_start: 0.8723 (mmp-170) cc_final: 0.8386 (tpp-160) REVERT: B 205 ASN cc_start: 0.8811 (m-40) cc_final: 0.8362 (p0) REVERT: B 268 LEU cc_start: 0.9425 (tp) cc_final: 0.9183 (tp) REVERT: B 366 LYS cc_start: 0.8792 (mppt) cc_final: 0.8379 (mmmt) REVERT: B 409 TYR cc_start: 0.8276 (m-10) cc_final: 0.6978 (m-10) REVERT: B 562 MET cc_start: 0.9009 (tpp) cc_final: 0.8740 (tpp) REVERT: B 574 MET cc_start: 0.8849 (mtm) cc_final: 0.8621 (mtm) REVERT: B 592 PHE cc_start: 0.8664 (t80) cc_final: 0.8364 (t80) REVERT: B 595 ILE cc_start: 0.9393 (mm) cc_final: 0.9039 (tp) REVERT: B 672 MET cc_start: 0.9067 (tmm) cc_final: 0.8738 (tmm) REVERT: C 188 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8514 (mmp80) REVERT: C 205 ASN cc_start: 0.8768 (m-40) cc_final: 0.8246 (p0) REVERT: C 268 LEU cc_start: 0.9419 (tp) cc_final: 0.9179 (tp) REVERT: C 366 LYS cc_start: 0.8864 (mppt) cc_final: 0.8474 (mmmt) REVERT: C 497 ILE cc_start: 0.9093 (tp) cc_final: 0.8871 (tt) REVERT: C 562 MET cc_start: 0.8998 (tpp) cc_final: 0.8718 (tpp) REVERT: C 572 MET cc_start: 0.8447 (tpp) cc_final: 0.7832 (mmm) REVERT: C 574 MET cc_start: 0.8834 (mtm) cc_final: 0.8607 (mtm) REVERT: C 592 PHE cc_start: 0.8701 (t80) cc_final: 0.8453 (t80) REVERT: C 595 ILE cc_start: 0.9390 (mm) cc_final: 0.9020 (tp) REVERT: C 672 MET cc_start: 0.9061 (tmm) cc_final: 0.8741 (tmm) REVERT: D 188 ARG cc_start: 0.8720 (mmp-170) cc_final: 0.8496 (mmp80) REVERT: D 205 ASN cc_start: 0.8816 (m-40) cc_final: 0.8358 (p0) REVERT: D 268 LEU cc_start: 0.9422 (tp) cc_final: 0.9173 (tp) REVERT: D 366 LYS cc_start: 0.8846 (mppt) cc_final: 0.8416 (mmmt) REVERT: D 497 ILE cc_start: 0.9089 (tp) cc_final: 0.8883 (tt) REVERT: D 562 MET cc_start: 0.8993 (tpp) cc_final: 0.8682 (tpp) REVERT: D 574 MET cc_start: 0.8863 (mtm) cc_final: 0.8616 (mtm) REVERT: D 592 PHE cc_start: 0.8690 (t80) cc_final: 0.8438 (t80) REVERT: D 595 ILE cc_start: 0.9397 (mm) cc_final: 0.9066 (tp) REVERT: D 672 MET cc_start: 0.9079 (tmm) cc_final: 0.8743 (tmm) REVERT: D 677 MET cc_start: 0.8556 (ttm) cc_final: 0.7923 (ttm) outliers start: 4 outliers final: 4 residues processed: 536 average time/residue: 0.1200 time to fit residues: 98.8365 Evaluate side-chains 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 371 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 561 ASN A 580 GLN A 671 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 570 GLN B 580 GLN B 671 ASN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 561 ASN C 570 GLN C 580 GLN C 671 ASN ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 570 GLN D 580 GLN D 671 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097983 restraints weight = 39586.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100314 restraints weight = 25346.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101969 restraints weight = 18290.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103104 restraints weight = 14350.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103995 restraints weight = 11996.832| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19320 Z= 0.126 Angle : 0.653 9.015 26120 Z= 0.331 Chirality : 0.041 0.183 3000 Planarity : 0.005 0.069 3236 Dihedral : 4.986 21.241 2524 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.39 % Allowed : 6.15 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.57 (0.16), residues: 2288 helix: -0.86 (0.13), residues: 1468 sheet: -1.44 (0.82), residues: 40 loop : -3.31 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 716 TYR 0.013 0.001 TYR A 661 PHE 0.019 0.001 PHE B 656 TRP 0.006 0.001 TRP A 739 HIS 0.002 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00259 (19320) covalent geometry : angle 0.65343 (26120) hydrogen bonds : bond 0.04287 ( 996) hydrogen bonds : angle 4.30634 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 504 time to evaluate : 0.610 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: A 159 MET cc_start: 0.6389 (mpp) cc_final: 0.6013 (mpp) REVERT: A 246 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7531 (ttpp) REVERT: A 366 LYS cc_start: 0.8837 (mppt) cc_final: 0.8335 (mmmt) REVERT: A 431 MET cc_start: 0.8632 (ttm) cc_final: 0.8223 (ttm) REVERT: A 527 PHE cc_start: 0.8126 (t80) cc_final: 0.7888 (t80) REVERT: A 555 MET cc_start: 0.8145 (tpp) cc_final: 0.7838 (tpp) REVERT: A 561 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8735 (t0) REVERT: A 562 MET cc_start: 0.9049 (tpp) cc_final: 0.8795 (tpp) REVERT: A 595 ILE cc_start: 0.9343 (mm) cc_final: 0.9025 (tp) REVERT: A 677 MET cc_start: 0.8280 (ttt) cc_final: 0.7969 (tpp) REVERT: A 740 THR cc_start: 0.7527 (m) cc_final: 0.7271 (p) REVERT: B 159 MET cc_start: 0.6545 (mpp) cc_final: 0.6092 (mpp) REVERT: B 205 ASN cc_start: 0.8600 (m-40) cc_final: 0.8382 (p0) REVERT: B 246 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7392 (ttpp) REVERT: B 366 LYS cc_start: 0.8826 (mppt) cc_final: 0.8390 (mmmt) REVERT: B 402 SER cc_start: 0.9077 (t) cc_final: 0.8843 (p) REVERT: B 431 MET cc_start: 0.8651 (ttm) cc_final: 0.8217 (ttm) REVERT: B 527 PHE cc_start: 0.8229 (t80) cc_final: 0.7974 (t80) REVERT: B 561 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8747 (t0) REVERT: B 562 MET cc_start: 0.9089 (tpp) cc_final: 0.8819 (tpp) REVERT: B 595 ILE cc_start: 0.9348 (mm) cc_final: 0.9007 (tp) REVERT: B 740 THR cc_start: 0.7447 (m) cc_final: 0.7153 (t) REVERT: C 159 MET cc_start: 0.6412 (mpp) cc_final: 0.6036 (mpp) REVERT: C 205 ASN cc_start: 0.8613 (m-40) cc_final: 0.8360 (p0) REVERT: C 246 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7442 (ttpp) REVERT: C 279 GLN cc_start: 0.7297 (tp40) cc_final: 0.6920 (tp-100) REVERT: C 283 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6696 (mt-10) REVERT: C 366 LYS cc_start: 0.8842 (mppt) cc_final: 0.8458 (mmmt) REVERT: C 402 SER cc_start: 0.9063 (t) cc_final: 0.8851 (p) REVERT: C 431 MET cc_start: 0.8708 (ttm) cc_final: 0.8308 (ttm) REVERT: C 497 ILE cc_start: 0.9062 (tp) cc_final: 0.8766 (tt) REVERT: C 561 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8724 (t0) REVERT: C 562 MET cc_start: 0.9102 (tpp) cc_final: 0.8796 (tpp) REVERT: C 595 ILE cc_start: 0.9346 (mm) cc_final: 0.9002 (tp) REVERT: C 743 LYS cc_start: 0.7865 (mttt) cc_final: 0.7628 (mmtt) REVERT: D 159 MET cc_start: 0.6532 (mpp) cc_final: 0.6076 (mpp) REVERT: D 205 ASN cc_start: 0.8589 (m-40) cc_final: 0.8376 (p0) REVERT: D 246 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7429 (ttpp) REVERT: D 268 LEU cc_start: 0.9206 (tp) cc_final: 0.8993 (tp) REVERT: D 366 LYS cc_start: 0.8870 (mppt) cc_final: 0.8401 (mmmt) REVERT: D 402 SER cc_start: 0.9069 (t) cc_final: 0.8853 (p) REVERT: D 431 MET cc_start: 0.8650 (ttm) cc_final: 0.8259 (ttm) REVERT: D 497 ILE cc_start: 0.9068 (tp) cc_final: 0.8766 (tt) REVERT: D 555 MET cc_start: 0.8151 (tpp) cc_final: 0.7848 (tpp) REVERT: D 561 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8755 (t0) REVERT: D 562 MET cc_start: 0.9095 (tpp) cc_final: 0.8804 (tpp) REVERT: D 595 ILE cc_start: 0.9357 (mm) cc_final: 0.8999 (tp) REVERT: D 740 THR cc_start: 0.7482 (m) cc_final: 0.7170 (t) outliers start: 8 outliers final: 4 residues processed: 512 average time/residue: 0.1087 time to fit residues: 89.8658 Evaluate side-chains 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 367 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 61.4253 > 50: distance: 34 - 52: 4.107 distance: 38 - 61: 5.012 distance: 44 - 72: 10.027 distance: 47 - 52: 6.210 distance: 48 - 81: 6.103 distance: 52 - 53: 3.023 distance: 53 - 54: 7.780 distance: 53 - 56: 15.290 distance: 54 - 55: 7.367 distance: 54 - 61: 9.541 distance: 56 - 57: 9.029 distance: 58 - 59: 6.377 distance: 58 - 60: 3.413 distance: 61 - 62: 4.585 distance: 62 - 65: 8.994 distance: 63 - 64: 17.710 distance: 63 - 72: 4.359 distance: 65 - 66: 6.651 distance: 66 - 67: 3.681 distance: 66 - 68: 8.318 distance: 67 - 69: 4.211 distance: 68 - 70: 3.123 distance: 69 - 71: 4.464 distance: 72 - 73: 5.031 distance: 73 - 74: 8.350 distance: 73 - 76: 12.078 distance: 74 - 75: 23.053 distance: 74 - 81: 17.909 distance: 76 - 77: 14.134 distance: 77 - 78: 13.098 distance: 78 - 79: 21.657 distance: 78 - 80: 7.186 distance: 81 - 82: 12.114 distance: 82 - 83: 24.575 distance: 82 - 85: 9.291 distance: 83 - 84: 19.272 distance: 83 - 90: 18.715 distance: 85 - 86: 27.041 distance: 86 - 87: 23.730 distance: 87 - 88: 12.316 distance: 88 - 89: 18.878 distance: 90 - 91: 27.247 distance: 91 - 92: 17.074 distance: 91 - 94: 11.863 distance: 92 - 93: 20.497 distance: 92 - 98: 17.774 distance: 94 - 95: 16.293 distance: 95 - 96: 31.180 distance: 96 - 97: 30.624 distance: 98 - 99: 15.696 distance: 99 - 100: 29.120 distance: 99 - 102: 21.565 distance: 100 - 101: 29.974 distance: 100 - 106: 18.942 distance: 102 - 103: 27.012 distance: 103 - 104: 20.514 distance: 103 - 105: 19.718 distance: 106 - 107: 16.642 distance: 106 - 112: 24.878 distance: 107 - 108: 9.239 distance: 107 - 110: 12.911 distance: 108 - 109: 53.151 distance: 108 - 113: 20.847 distance: 110 - 111: 7.922 distance: 111 - 112: 22.137 distance: 113 - 114: 11.139 distance: 114 - 115: 16.233 distance: 114 - 117: 25.862 distance: 115 - 116: 20.824 distance: 115 - 122: 14.552 distance: 117 - 118: 30.013 distance: 118 - 119: 18.485 distance: 119 - 120: 22.231 distance: 119 - 121: 19.121 distance: 122 - 123: 21.211 distance: 123 - 124: 25.400 distance: 123 - 126: 23.368 distance: 124 - 125: 25.352 distance: 124 - 136: 25.783 distance: 126 - 127: 28.936 distance: 127 - 128: 28.005 distance: 127 - 129: 19.442 distance: 128 - 130: 5.579 distance: 129 - 131: 14.539 distance: 129 - 132: 12.045 distance: 130 - 131: 6.419 distance: 131 - 133: 10.028 distance: 132 - 134: 7.827 distance: 133 - 135: 5.612 distance: 134 - 135: 12.069 distance: 136 - 137: 24.106 distance: 137 - 138: 37.199 distance: 137 - 140: 14.984 distance: 138 - 139: 37.756 distance: 138 - 144: 19.401 distance: 140 - 141: 5.458 distance: 141 - 142: 15.107 distance: 141 - 143: 9.306