Starting phenix.real_space_refine on Sun Aug 24 12:27:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xew_33161/08_2025/7xew_33161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xew_33161/08_2025/7xew_33161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xew_33161/08_2025/7xew_33161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xew_33161/08_2025/7xew_33161.map" model { file = "/net/cci-nas-00/data/ceres_data/7xew_33161/08_2025/7xew_33161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xew_33161/08_2025/7xew_33161.cif" } resolution = 2.59 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13080 2.51 5 N 3368 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19988 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4997 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 4.25, per 1000 atoms: 0.21 Number of scatterers: 19988 At special positions: 0 Unit cell: (157.17, 157.17, 115.596, 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 108 16.00 O 3432 8.00 N 3368 7.00 C 13080 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: 1.65 Conformation dependent library (CDL) restraints added in 757.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 62.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU A 86 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.559A pdb=" N VAL A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.561A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.781A pdb=" N ASP A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 373 through 408 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 455 through 458 removed outlier: 3.994A pdb=" N ILE A 458 " --> pdb=" O ARG A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.935A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 514 through 532 removed outlier: 3.670A pdb=" N LEU A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.565A pdb=" N THR A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 631 through 668 removed outlier: 5.925A pdb=" N THR A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 714 removed outlier: 3.768A pdb=" N THR A 713 " --> pdb=" O TRP A 710 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 714 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU B 86 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.559A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.561A pdb=" N GLU B 226 " --> pdb=" O THR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 281 through 285 removed outlier: 3.781A pdb=" N ASP B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 285' Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 373 through 408 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 455 through 458 removed outlier: 3.994A pdb=" N ILE B 458 " --> pdb=" O ARG B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.934A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 514 through 532 removed outlier: 3.670A pdb=" N LEU B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 Processing helix chain 'B' and resid 587 through 601 removed outlier: 3.565A pdb=" N THR B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 631 through 668 removed outlier: 5.924A pdb=" N THR B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 714 removed outlier: 3.768A pdb=" N THR B 713 " --> pdb=" O TRP B 710 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 714 " --> pdb=" O GLU B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU C 86 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.558A pdb=" N VAL C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.562A pdb=" N GLU C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 Processing helix chain 'C' and resid 281 through 285 removed outlier: 3.781A pdb=" N ASP C 284 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 281 through 285' Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 373 through 408 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 455 through 458 removed outlier: 3.995A pdb=" N ILE C 458 " --> pdb=" O ARG C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.935A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 514 through 532 removed outlier: 3.669A pdb=" N LEU C 532 " --> pdb=" O ILE C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 Processing helix chain 'C' and resid 587 through 601 removed outlier: 3.565A pdb=" N THR C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 631 through 668 removed outlier: 5.926A pdb=" N THR C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 714 removed outlier: 3.768A pdb=" N THR C 713 " --> pdb=" O TRP C 710 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 714 " --> pdb=" O GLU C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU D 86 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.559A pdb=" N VAL D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.561A pdb=" N GLU D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.782A pdb=" N ASP D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 281 through 285' Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 373 through 408 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 455 through 458 removed outlier: 3.995A pdb=" N ILE D 458 " --> pdb=" O ARG D 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 455 through 458' Processing helix chain 'D' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 506 removed outlier: 3.935A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 514 through 532 removed outlier: 3.669A pdb=" N LEU D 532 " --> pdb=" O ILE D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 Processing helix chain 'D' and resid 587 through 601 removed outlier: 3.566A pdb=" N THR D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 631 through 668 removed outlier: 5.925A pdb=" N THR D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 714 removed outlier: 3.767A pdb=" N THR D 713 " --> pdb=" O TRP D 710 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 714 " --> pdb=" O GLU D 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 330 removed outlier: 7.093A pdb=" N VAL A 335 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS A 329 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 324 through 330 removed outlier: 7.093A pdb=" N VAL B 335 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS B 329 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 330 removed outlier: 7.092A pdb=" N VAL C 335 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS C 329 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 333 " --> pdb=" O CYS C 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 324 through 330 removed outlier: 7.092A pdb=" N VAL D 335 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS D 329 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 333 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3168 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: 2.17 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: 5825 1.34 - 1.45: 3418 1.45 - 1.57: 11093 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 20496 Sorted by residual: bond pdb=" CA ILE C 385 " pdb=" CB ILE C 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.52e+00 bond pdb=" CA ILE A 385 " pdb=" CB ILE A 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.36e+00 bond pdb=" CA ILE B 385 " pdb=" CB ILE B 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.15e+00 bond pdb=" CA ILE D 385 " pdb=" CB ILE D 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.11e+00 bond pdb=" CG PRO D 694 " pdb=" CD PRO D 694 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 2.99e+00 ... (remaining 20491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 27121 1.99 - 3.98: 595 3.98 - 5.97: 87 5.97 - 7.96: 5 7.96 - 9.95: 4 Bond angle restraints: 27812 Sorted by residual: angle pdb=" N VAL C 148 " pdb=" CA VAL C 148 " pdb=" C VAL C 148 " ideal model delta sigma weight residual 113.71 107.79 5.92 9.50e-01 1.11e+00 3.88e+01 angle pdb=" N VAL B 148 " pdb=" CA VAL B 148 " pdb=" C VAL B 148 " ideal model delta sigma weight residual 113.71 107.80 5.91 9.50e-01 1.11e+00 3.88e+01 angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 113.71 107.83 5.88 9.50e-01 1.11e+00 3.84e+01 angle pdb=" N VAL D 148 " pdb=" CA VAL D 148 " pdb=" C VAL D 148 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL D 368 " pdb=" CA VAL D 368 " pdb=" C VAL D 368 " ideal model delta sigma weight residual 106.21 110.91 -4.70 1.07e+00 8.73e-01 1.93e+01 ... (remaining 27807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 10655 15.29 - 30.59: 1025 30.59 - 45.88: 280 45.88 - 61.18: 44 61.18 - 76.47: 16 Dihedral angle restraints: 12020 sinusoidal: 4852 harmonic: 7168 Sorted by residual: dihedral pdb=" CA PRO B 146 " pdb=" C PRO B 146 " pdb=" N LEU B 147 " pdb=" CA LEU B 147 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N LEU A 147 " pdb=" CA LEU A 147 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PRO D 146 " pdb=" C PRO D 146 " pdb=" N LEU D 147 " pdb=" CA LEU D 147 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 12017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2233 0.040 - 0.080: 687 0.080 - 0.119: 199 0.119 - 0.159: 17 0.159 - 0.199: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA VAL C 369 " pdb=" N VAL C 369 " pdb=" C VAL C 369 " pdb=" CB VAL C 369 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 3137 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 693 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO D 694 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 694 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 694 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 693 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO C 694 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 694 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 694 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 693 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 694 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " 0.037 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2256 2.75 - 3.29: 20079 3.29 - 3.82: 33531 3.82 - 4.36: 37806 4.36 - 4.90: 65770 Nonbonded interactions: 159442 Sorted by model distance: nonbonded pdb=" OE1 GLU B 711 " pdb=" NZ LYS C 216 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS A 216 " pdb=" OE1 GLU D 711 " model vdw 2.217 3.120 nonbonded pdb=" OE1 GLU C 711 " pdb=" NZ LYS D 216 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLU A 711 " pdb=" NZ LYS B 216 " model vdw 2.247 3.120 nonbonded pdb=" NH1 ARG B 275 " pdb=" OH TYR B 318 " model vdw 2.249 3.120 ... (remaining 159437 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 individual isotropic 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: 0.740 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: 0.060 Set scattering table: 0.060 Process input model: 16.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.003 0.060 20496 Z= 0.172 Angle : 0.704 9.954 27812 Z= 0.426 Chirality : 0.042 0.199 3140 Planarity : 0.005 0.067 3432 Dihedral : 13.276 76.474 7396 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.47 % Favored : 94.04 % Rotamer: Outliers : 1.10 % Allowed : 0.37 % Favored : 98.53 % 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: 0.26 (0.18), residues: 2432 helix: 1.84 (0.14), residues: 1432 sheet: -2.98 (0.42), residues: 84 loop : -2.36 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 74 TYR 0.016 0.002 TYR D 539 PHE 0.014 0.001 PHE D 525 TRP 0.010 0.001 TRP C 346 HIS 0.015 0.002 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00342 (20496) covalent geometry : angle 0.70430 (27812) hydrogen bonds : bond 0.12719 ( 1072) hydrogen bonds : angle 5.32093 ( 3168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 331 time to evaluate : 0.556 Fit side-chains REVERT: B 136 GLN cc_start: 0.8609 (mp10) cc_final: 0.8369 (mp10) REVERT: B 684 LEU cc_start: 0.8505 (mt) cc_final: 0.8302 (mt) REVERT: C 463 MET cc_start: 0.5612 (tpt) cc_final: 0.5398 (mmm) REVERT: D 136 GLN cc_start: 0.8567 (mp10) cc_final: 0.8323 (mp10) outliers start: 24 outliers final: 8 residues processed: 339 average time/residue: 0.4937 time to fit residues: 190.8873 Evaluate side-chains 211 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 600 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084593 restraints weight = 35598.093| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.62 r_work: 0.3058 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20496 Z= 0.131 Angle : 0.588 8.468 27812 Z= 0.302 Chirality : 0.039 0.169 3140 Planarity : 0.004 0.052 3432 Dihedral : 6.108 98.239 2716 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.28 % Favored : 95.56 % Rotamer: Outliers : 2.85 % Allowed : 10.29 % Favored : 86.86 % 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: 0.74 (0.18), residues: 2432 helix: 2.23 (0.14), residues: 1448 sheet: -2.51 (0.42), residues: 84 loop : -2.29 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.014 0.001 TYR C 539 PHE 0.013 0.001 PHE C 402 TRP 0.009 0.001 TRP C 173 HIS 0.012 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00283 (20496) covalent geometry : angle 0.58840 (27812) hydrogen bonds : bond 0.04697 ( 1072) hydrogen bonds : angle 3.95186 ( 3168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8899 (mm) cc_final: 0.8590 (mm) REVERT: A 371 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: A 704 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6483 (pp20) REVERT: B 188 ARG cc_start: 0.8283 (mpp80) cc_final: 0.7780 (ttm-80) REVERT: B 371 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: B 684 LEU cc_start: 0.8682 (mt) cc_final: 0.8309 (mp) REVERT: B 696 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6755 (tp30) REVERT: B 704 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: C 371 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: C 463 MET cc_start: 0.5867 (tpt) cc_final: 0.5616 (mmm) REVERT: C 704 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6347 (pp20) REVERT: D 188 ARG cc_start: 0.8331 (mpp80) cc_final: 0.7769 (ttm-80) REVERT: D 371 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: D 704 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6532 (pp20) outliers start: 62 outliers final: 33 residues processed: 298 average time/residue: 0.5221 time to fit residues: 179.0299 Evaluate side-chains 256 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 156 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.074677 restraints weight = 36015.616| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.64 r_work: 0.2885 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 20496 Z= 0.348 Angle : 0.736 7.627 27812 Z= 0.381 Chirality : 0.045 0.210 3140 Planarity : 0.006 0.052 3432 Dihedral : 6.197 88.666 2716 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.20 % Rotamer: Outliers : 5.88 % Allowed : 11.63 % Favored : 82.49 % 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: 0.31 (0.17), residues: 2432 helix: 1.80 (0.13), residues: 1452 sheet: -1.66 (0.43), residues: 88 loop : -2.44 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.026 0.003 TYR B 510 PHE 0.032 0.003 PHE C 402 TRP 0.015 0.002 TRP C 173 HIS 0.011 0.002 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00825 (20496) covalent geometry : angle 0.73551 (27812) hydrogen bonds : bond 0.07345 ( 1072) hydrogen bonds : angle 4.25133 ( 3168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 205 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLN cc_start: 0.8617 (pm20) cc_final: 0.8341 (mm110) REVERT: A 371 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: A 628 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 281 GLN cc_start: 0.8607 (pm20) cc_final: 0.8324 (mm110) REVERT: B 371 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: B 628 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8906 (p) REVERT: C 117 MET cc_start: 0.7749 (mtt) cc_final: 0.7541 (mtt) REVERT: C 135 LEU cc_start: 0.8978 (mm) cc_final: 0.8709 (mt) REVERT: C 281 GLN cc_start: 0.8629 (pm20) cc_final: 0.8382 (mm110) REVERT: C 371 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: C 387 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8338 (ttm110) REVERT: C 463 MET cc_start: 0.6080 (tpt) cc_final: 0.5775 (mmm) REVERT: C 628 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8915 (p) REVERT: D 135 LEU cc_start: 0.9080 (mm) cc_final: 0.8875 (mm) REVERT: D 281 GLN cc_start: 0.8597 (pm20) cc_final: 0.8319 (mm110) REVERT: D 371 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: D 628 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8907 (p) outliers start: 128 outliers final: 53 residues processed: 301 average time/residue: 0.4676 time to fit residues: 162.8406 Evaluate side-chains 251 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 0.0470 chunk 173 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 HIS B 143 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.118645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.081460 restraints weight = 35839.963| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.63 r_work: 0.3011 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20496 Z= 0.118 Angle : 0.559 13.117 27812 Z= 0.286 Chirality : 0.039 0.177 3140 Planarity : 0.004 0.051 3432 Dihedral : 5.784 88.034 2716 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 3.40 % Allowed : 16.04 % Favored : 80.56 % 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: 0.77 (0.18), residues: 2432 helix: 2.18 (0.14), residues: 1452 sheet: -1.35 (0.43), residues: 88 loop : -2.29 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.018 0.001 TYR D 93 PHE 0.010 0.001 PHE D 525 TRP 0.011 0.001 TRP A 173 HIS 0.009 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00237 (20496) covalent geometry : angle 0.55856 (27812) hydrogen bonds : bond 0.04287 ( 1072) hydrogen bonds : angle 3.80094 ( 3168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7909 (pp) REVERT: A 188 ARG cc_start: 0.8404 (mpp80) cc_final: 0.8143 (mpp80) REVERT: A 281 GLN cc_start: 0.8591 (pm20) cc_final: 0.8345 (mm110) REVERT: A 704 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6268 (pp20) REVERT: B 123 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7831 (pp) REVERT: B 135 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 188 ARG cc_start: 0.8535 (mpp80) cc_final: 0.8193 (mpp80) REVERT: B 281 GLN cc_start: 0.8592 (pm20) cc_final: 0.8349 (mm110) REVERT: B 704 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6277 (pp20) REVERT: C 123 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7826 (pp) REVERT: C 135 LEU cc_start: 0.8904 (mm) cc_final: 0.8613 (mt) REVERT: C 281 GLN cc_start: 0.8598 (pm20) cc_final: 0.8357 (mm110) REVERT: C 463 MET cc_start: 0.5926 (tpt) cc_final: 0.5623 (mmm) REVERT: C 704 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6247 (pp20) REVERT: D 123 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7773 (pp) REVERT: D 135 LEU cc_start: 0.9019 (mm) cc_final: 0.8814 (mm) REVERT: D 188 ARG cc_start: 0.8536 (mpp80) cc_final: 0.8187 (mpp80) REVERT: D 281 GLN cc_start: 0.8577 (pm20) cc_final: 0.8333 (mm110) REVERT: D 704 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6274 (pp20) outliers start: 74 outliers final: 30 residues processed: 279 average time/residue: 0.4648 time to fit residues: 149.6768 Evaluate side-chains 237 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 161 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.117289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080085 restraints weight = 35691.597| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.62 r_work: 0.2983 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20496 Z= 0.142 Angle : 0.598 14.512 27812 Z= 0.297 Chirality : 0.039 0.424 3140 Planarity : 0.004 0.064 3432 Dihedral : 5.696 88.107 2716 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 5.06 % Allowed : 15.72 % Favored : 79.23 % 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: 0.88 (0.18), residues: 2432 helix: 2.23 (0.14), residues: 1448 sheet: -0.90 (0.48), residues: 88 loop : -2.20 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 72 TYR 0.011 0.001 TYR B 93 PHE 0.012 0.001 PHE C 525 TRP 0.010 0.001 TRP A 173 HIS 0.008 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00318 (20496) covalent geometry : angle 0.59799 (27812) hydrogen bonds : bond 0.04673 ( 1072) hydrogen bonds : angle 3.84651 ( 3168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 218 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7901 (pp) REVERT: A 188 ARG cc_start: 0.8440 (mpp80) cc_final: 0.8208 (mpp80) REVERT: A 281 GLN cc_start: 0.8571 (pm20) cc_final: 0.8326 (mm110) REVERT: A 556 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6722 (pp20) REVERT: A 628 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8984 (p) REVERT: A 704 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6398 (pp20) REVERT: B 123 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7829 (pp) REVERT: B 188 ARG cc_start: 0.8536 (mpp80) cc_final: 0.8183 (mpp80) REVERT: B 281 GLN cc_start: 0.8594 (pm20) cc_final: 0.8332 (mm110) REVERT: B 556 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6829 (pp20) REVERT: B 628 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 704 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: C 123 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7769 (pp) REVERT: C 281 GLN cc_start: 0.8601 (pm20) cc_final: 0.8378 (mm110) REVERT: C 463 MET cc_start: 0.5838 (tpt) cc_final: 0.5557 (mmm) REVERT: C 556 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6854 (pp20) REVERT: C 628 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8990 (p) REVERT: C 704 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6393 (pp20) REVERT: D 123 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7795 (pp) REVERT: D 135 LEU cc_start: 0.8958 (mm) cc_final: 0.8689 (mm) REVERT: D 188 ARG cc_start: 0.8548 (mpp80) cc_final: 0.8193 (mpp80) REVERT: D 281 GLN cc_start: 0.8575 (pm20) cc_final: 0.8334 (mm110) REVERT: D 556 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6751 (pp20) REVERT: D 628 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8994 (p) REVERT: D 704 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7118 (pt0) outliers start: 110 outliers final: 55 residues processed: 297 average time/residue: 0.4330 time to fit residues: 150.7712 Evaluate side-chains 266 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 635 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 189 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079469 restraints weight = 35626.281| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.62 r_work: 0.2974 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20496 Z= 0.148 Angle : 0.610 15.157 27812 Z= 0.299 Chirality : 0.042 0.495 3140 Planarity : 0.004 0.063 3432 Dihedral : 5.679 87.119 2716 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.39 % Rotamer: Outliers : 5.65 % Allowed : 15.76 % Favored : 78.58 % 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: 0.93 (0.18), residues: 2432 helix: 2.21 (0.14), residues: 1452 sheet: -0.58 (0.50), residues: 88 loop : -2.13 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.011 0.001 TYR B 93 PHE 0.012 0.001 PHE C 402 TRP 0.011 0.001 TRP A 173 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00336 (20496) covalent geometry : angle 0.60988 (27812) hydrogen bonds : bond 0.04768 ( 1072) hydrogen bonds : angle 3.84055 ( 3168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 213 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7876 (pp) REVERT: A 188 ARG cc_start: 0.8524 (mpp80) cc_final: 0.8301 (mpp80) REVERT: A 556 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6686 (pp20) REVERT: A 628 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8963 (p) REVERT: A 704 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7033 (pt0) REVERT: B 93 TYR cc_start: 0.7412 (t80) cc_final: 0.7172 (t80) REVERT: B 99 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6696 (tmmt) REVERT: B 123 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7812 (pp) REVERT: B 556 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6749 (pp20) REVERT: B 628 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8955 (p) REVERT: B 704 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: C 71 ASP cc_start: 0.8096 (p0) cc_final: 0.7788 (p0) REVERT: C 123 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7891 (pp) REVERT: C 188 ARG cc_start: 0.8426 (mpp80) cc_final: 0.8147 (mpp80) REVERT: C 463 MET cc_start: 0.5912 (tpt) cc_final: 0.5592 (mmm) REVERT: C 556 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6764 (pp20) REVERT: C 628 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 704 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: D 93 TYR cc_start: 0.7470 (t80) cc_final: 0.7231 (t80) REVERT: D 99 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6743 (tmmt) REVERT: D 123 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7858 (pp) REVERT: D 135 LEU cc_start: 0.8992 (mm) cc_final: 0.8791 (mm) REVERT: D 281 GLN cc_start: 0.8594 (pm20) cc_final: 0.8392 (mm110) REVERT: D 556 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6759 (pp20) REVERT: D 628 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8960 (p) REVERT: D 704 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7120 (pt0) outliers start: 123 outliers final: 54 residues processed: 308 average time/residue: 0.4490 time to fit residues: 161.4560 Evaluate side-chains 276 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 635 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 0.0370 chunk 42 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN B 136 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.080194 restraints weight = 35652.458| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.61 r_work: 0.2992 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20496 Z= 0.129 Angle : 0.611 15.732 27812 Z= 0.295 Chirality : 0.042 0.499 3140 Planarity : 0.004 0.061 3432 Dihedral : 4.280 46.133 2704 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.15 % Favored : 95.68 % Rotamer: Outliers : 4.50 % Allowed : 16.87 % Favored : 78.63 % 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: 1.00 (0.18), residues: 2432 helix: 2.26 (0.14), residues: 1452 sheet: -0.40 (0.50), residues: 88 loop : -2.09 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.023 0.001 TYR A 93 PHE 0.011 0.001 PHE D 525 TRP 0.015 0.001 TRP B 173 HIS 0.007 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00285 (20496) covalent geometry : angle 0.61109 (27812) hydrogen bonds : bond 0.04482 ( 1072) hydrogen bonds : angle 3.80104 ( 3168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 216 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7847 (pp) REVERT: A 556 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6679 (pp20) REVERT: A 704 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6344 (pp20) REVERT: B 123 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 188 ARG cc_start: 0.8583 (mpp80) cc_final: 0.8218 (tpp80) REVERT: B 556 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6761 (pp20) REVERT: B 704 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: C 123 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7862 (pp) REVERT: C 188 ARG cc_start: 0.8448 (mpp80) cc_final: 0.8202 (mpp80) REVERT: C 463 MET cc_start: 0.5980 (tpt) cc_final: 0.5645 (mmm) REVERT: C 556 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6775 (pp20) REVERT: C 704 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6285 (pp20) REVERT: D 123 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7820 (pp) REVERT: D 135 LEU cc_start: 0.9034 (mm) cc_final: 0.8775 (mm) REVERT: D 139 ARG cc_start: 0.8745 (pmt-80) cc_final: 0.8541 (pmt-80) REVERT: D 188 ARG cc_start: 0.8604 (mpp80) cc_final: 0.8232 (tpp80) REVERT: D 556 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6775 (pp20) REVERT: D 611 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8108 (pp) REVERT: D 704 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7090 (pt0) outliers start: 98 outliers final: 48 residues processed: 291 average time/residue: 0.4716 time to fit residues: 160.2549 Evaluate side-chains 267 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 635 MET Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 127 optimal weight: 7.9990 chunk 125 optimal weight: 0.0570 chunk 138 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.0040 chunk 179 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 overall best weight: 0.5112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083396 restraints weight = 35822.542| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.62 r_work: 0.3041 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20496 Z= 0.109 Angle : 0.598 14.693 27812 Z= 0.288 Chirality : 0.040 0.419 3140 Planarity : 0.004 0.062 3432 Dihedral : 4.216 47.094 2704 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 4.04 % Allowed : 17.92 % Favored : 78.03 % 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: 1.09 (0.18), residues: 2432 helix: 2.25 (0.14), residues: 1476 sheet: -0.26 (0.49), residues: 88 loop : -2.05 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.008 0.001 TYR B 93 PHE 0.009 0.001 PHE C 525 TRP 0.018 0.001 TRP A 173 HIS 0.007 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00228 (20496) covalent geometry : angle 0.59769 (27812) hydrogen bonds : bond 0.03746 ( 1072) hydrogen bonds : angle 3.69403 ( 3168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 232 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6723 (pp20) REVERT: A 628 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 704 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6131 (pp20) REVERT: B 123 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (pp) REVERT: B 188 ARG cc_start: 0.8569 (mpp80) cc_final: 0.8232 (tpp80) REVERT: B 556 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6855 (pp20) REVERT: B 628 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8978 (p) REVERT: B 676 LYS cc_start: 0.7084 (pptt) cc_final: 0.6874 (pttp) REVERT: B 704 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6171 (pp20) REVERT: C 71 ASP cc_start: 0.8031 (p0) cc_final: 0.7737 (p0) REVERT: C 188 ARG cc_start: 0.8385 (mpp80) cc_final: 0.8180 (mpp80) REVERT: C 463 MET cc_start: 0.5878 (tpt) cc_final: 0.5517 (mmm) REVERT: C 556 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6870 (pp20) REVERT: C 626 LEU cc_start: 0.9411 (tp) cc_final: 0.9205 (OUTLIER) REVERT: C 628 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8988 (p) REVERT: C 704 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6190 (pp20) REVERT: D 123 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7767 (pp) REVERT: D 135 LEU cc_start: 0.9023 (mm) cc_final: 0.8781 (mm) REVERT: D 188 ARG cc_start: 0.8581 (mpp80) cc_final: 0.8261 (tpp80) REVERT: D 556 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6814 (pp20) REVERT: D 611 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8063 (pp) REVERT: D 628 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8988 (p) REVERT: D 704 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6235 (pp20) outliers start: 88 outliers final: 38 residues processed: 302 average time/residue: 0.4949 time to fit residues: 173.7022 Evaluate side-chains 264 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 635 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 122 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080322 restraints weight = 35451.850| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.62 r_work: 0.2991 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20496 Z= 0.146 Angle : 0.632 15.205 27812 Z= 0.304 Chirality : 0.042 0.425 3140 Planarity : 0.004 0.060 3432 Dihedral : 4.227 46.015 2704 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 3.26 % Allowed : 19.39 % Favored : 77.34 % 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: 1.02 (0.18), residues: 2432 helix: 2.19 (0.14), residues: 1480 sheet: 0.04 (0.52), residues: 88 loop : -2.13 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 275 TYR 0.015 0.001 TYR D 93 PHE 0.013 0.001 PHE C 402 TRP 0.019 0.001 TRP C 173 HIS 0.006 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00333 (20496) covalent geometry : angle 0.63232 (27812) hydrogen bonds : bond 0.04545 ( 1072) hydrogen bonds : angle 3.80142 ( 3168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7606 (pp) REVERT: A 556 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6693 (pp20) REVERT: A 628 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8918 (p) REVERT: A 704 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6333 (pp20) REVERT: B 123 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7812 (pp) REVERT: B 188 ARG cc_start: 0.8586 (mpp80) cc_final: 0.8258 (tpp80) REVERT: B 556 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6740 (pp20) REVERT: B 628 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8919 (p) REVERT: B 704 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7095 (pt0) REVERT: C 123 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7733 (pp) REVERT: C 188 ARG cc_start: 0.8475 (mpp80) cc_final: 0.8245 (mpp80) REVERT: C 463 MET cc_start: 0.5904 (tpt) cc_final: 0.5667 (mmm) REVERT: C 556 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6785 (pp20) REVERT: C 628 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 704 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6330 (pp20) REVERT: D 123 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7717 (pp) REVERT: D 188 ARG cc_start: 0.8643 (mpp80) cc_final: 0.8318 (tpp80) REVERT: D 556 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6748 (pp20) REVERT: D 611 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8133 (pp) REVERT: D 628 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8926 (p) REVERT: D 704 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6938 (pt0) outliers start: 71 outliers final: 42 residues processed: 278 average time/residue: 0.4896 time to fit residues: 157.2868 Evaluate side-chains 262 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 635 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6895 > 50: distance: 4 - 12: 3.069 distance: 79 - 98: 17.974 distance: 85 - 105: 5.615 distance: 90 - 111: 11.030 distance: 93 - 98: 18.313 distance: 94 - 117: 13.098 distance: 98 - 99: 26.179 distance: 99 - 100: 17.378 distance: 99 - 102: 8.672 distance: 100 - 101: 8.626 distance: 100 - 105: 14.614 distance: 101 - 125: 20.070 distance: 102 - 103: 43.101 distance: 102 - 104: 21.744 distance: 105 - 106: 6.946 distance: 106 - 107: 11.338 distance: 106 - 109: 15.858 distance: 107 - 108: 11.399 distance: 107 - 111: 6.200 distance: 109 - 110: 33.156 distance: 111 - 112: 4.936 distance: 112 - 113: 9.826 distance: 112 - 115: 7.161 distance: 113 - 114: 6.920 distance: 113 - 117: 9.830 distance: 114 - 140: 42.299 distance: 115 - 116: 6.269 distance: 117 - 118: 4.410 distance: 118 - 119: 10.268 distance: 118 - 121: 14.336 distance: 119 - 120: 26.555 distance: 119 - 125: 9.666 distance: 120 - 144: 23.103 distance: 121 - 122: 5.548 distance: 122 - 123: 6.853 distance: 122 - 124: 18.283 distance: 126 - 127: 5.261 distance: 126 - 129: 4.702 distance: 127 - 128: 15.796 distance: 127 - 132: 8.253 distance: 128 - 158: 25.152 distance: 129 - 130: 15.525 distance: 129 - 131: 5.195 distance: 133 - 134: 13.933 distance: 133 - 136: 7.101 distance: 134 - 135: 28.599 distance: 134 - 140: 22.521 distance: 135 - 166: 26.721 distance: 136 - 137: 8.507 distance: 137 - 138: 11.566 distance: 137 - 139: 17.620 distance: 141 - 142: 41.035 distance: 142 - 143: 16.043 distance: 142 - 144: 27.760 distance: 144 - 145: 14.253 distance: 145 - 146: 19.638 distance: 145 - 148: 13.612 distance: 146 - 147: 13.464 distance: 146 - 158: 24.183 distance: 148 - 149: 15.086 distance: 149 - 150: 16.273 distance: 149 - 151: 10.560 distance: 150 - 152: 19.602 distance: 151 - 153: 17.163 distance: 151 - 154: 19.309 distance: 152 - 153: 15.366 distance: 153 - 155: 14.640 distance: 154 - 156: 9.744 distance: 155 - 157: 21.724 distance: 156 - 157: 15.907 distance: 158 - 159: 10.291 distance: 159 - 160: 9.710 distance: 159 - 162: 9.703 distance: 160 - 161: 17.457 distance: 160 - 166: 16.571 distance: 162 - 163: 17.579 distance: 163 - 164: 13.330 distance: 163 - 165: 22.530 distance: 166 - 167: 12.980 distance: 167 - 168: 20.650 distance: 167 - 170: 23.409 distance: 168 - 169: 9.033 distance: 168 - 174: 5.091 distance: 170 - 171: 14.051 distance: 171 - 172: 10.746 distance: 171 - 173: 11.025 distance: 210 - 221: 3.024