Starting phenix.real_space_refine on Tue Oct 15 06:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/10_2024/7xew_33161.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/10_2024/7xew_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/10_2024/7xew_33161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/10_2024/7xew_33161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/10_2024/7xew_33161.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/10_2024/7xew_33161.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/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: C, B, D Time building chain proxies: 11.28, per 1000 atoms: 0.56 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: 5.05 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.91 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: 6.35 Time building geometry restraints manager: 5.74 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: 0.00 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: 0.620 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: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.870 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- 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= 0.221 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP C 346 HIS 0.015 0.002 HIS B 516 PHE 0.014 0.001 PHE D 525 TYR 0.016 0.002 TYR D 539 ARG 0.006 0.000 ARG C 74 *********************** 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 fitting. rotamer outliers: 24 poor density : 331 time to evaluate : 2.333 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: 1.1829 time to fit residues: 460.3560 Evaluate side-chains 211 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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 206 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20496 Z= 0.254 Angle : 0.614 8.112 27812 Z= 0.316 Chirality : 0.040 0.176 3140 Planarity : 0.004 0.052 3432 Dihedral : 6.226 97.975 2716 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 2.94 % Allowed : 10.94 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2432 helix: 2.12 (0.14), residues: 1448 sheet: -2.43 (0.42), residues: 84 loop : -2.44 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 173 HIS 0.013 0.002 HIS B 516 PHE 0.016 0.002 PHE C 402 TYR 0.015 0.002 TYR C 510 ARG 0.004 0.001 ARG A 307 *********************** 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 307 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 243 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8788 (tt) REVERT: A 135 LEU cc_start: 0.8937 (mm) cc_final: 0.8674 (mm) REVERT: A 704 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6630 (pt0) REVERT: B 684 LEU cc_start: 0.8693 (mt) cc_final: 0.8416 (mp) REVERT: B 696 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6671 (tp30) REVERT: B 704 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6572 (pt0) REVERT: C 434 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8974 (mm) REVERT: C 704 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6621 (pt0) REVERT: D 696 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6721 (tp30) REVERT: D 704 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6549 (pt0) outliers start: 64 outliers final: 34 residues processed: 287 average time/residue: 1.2367 time to fit residues: 406.4021 Evaluate side-chains 247 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 132 LEU 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 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 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 431 LEU Chi-restraints excluded: chain C residue 434 ILE 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 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 123 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 221 optimal weight: 8.9990 chunk 239 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 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 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20496 Z= 0.216 Angle : 0.569 12.385 27812 Z= 0.294 Chirality : 0.039 0.272 3140 Planarity : 0.004 0.052 3432 Dihedral : 4.175 34.315 2704 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 3.58 % Allowed : 13.69 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2432 helix: 2.19 (0.14), residues: 1452 sheet: -1.96 (0.37), residues: 112 loop : -2.42 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 173 HIS 0.011 0.001 HIS B 516 PHE 0.016 0.001 PHE C 402 TYR 0.010 0.001 TYR C 510 ARG 0.006 0.001 ARG C 188 *********************** 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 291 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 213 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8909 (mm) cc_final: 0.8684 (mt) REVERT: A 704 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6656 (pt0) REVERT: B 135 LEU cc_start: 0.8876 (mm) cc_final: 0.8595 (mt) REVERT: B 136 GLN cc_start: 0.8617 (mp10) cc_final: 0.8409 (mp10) REVERT: B 704 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6660 (pt0) REVERT: C 704 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: D 135 LEU cc_start: 0.9022 (mm) cc_final: 0.8681 (mm) REVERT: D 136 GLN cc_start: 0.8678 (mp10) cc_final: 0.8457 (mp10) REVERT: D 704 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6684 (pt0) outliers start: 78 outliers final: 42 residues processed: 268 average time/residue: 1.2069 time to fit residues: 372.3927 Evaluate side-chains 238 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 136 GLN 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 435 LEU 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 702 VAL Chi-restraints excluded: chain A residue 704 GLU 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 435 LEU 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 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 219 ASP 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 635 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 704 GLU 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 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 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 219 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 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 ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1761 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= 0.199 Angle : 0.586 13.820 27812 Z= 0.293 Chirality : 0.040 0.450 3140 Planarity : 0.004 0.051 3432 Dihedral : 4.164 38.076 2704 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.39 % Rotamer: Outliers : 4.23 % Allowed : 14.34 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2432 helix: 2.27 (0.14), residues: 1452 sheet: -1.48 (0.40), residues: 112 loop : -2.34 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 173 HIS 0.009 0.001 HIS B 516 PHE 0.013 0.001 PHE C 402 TYR 0.017 0.001 TYR D 93 ARG 0.006 0.000 ARG C 275 *********************** 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 288 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 196 time to evaluate : 2.202 Fit side-chains revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 704 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: B 123 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7782 (pp) REVERT: B 704 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6639 (pt0) REVERT: C 123 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7917 (pp) REVERT: C 188 ARG cc_start: 0.8117 (mpp80) cc_final: 0.7894 (mpp80) REVERT: C 704 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6553 (pt0) REVERT: D 123 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7742 (pp) REVERT: D 188 ARG cc_start: 0.8230 (mpp80) cc_final: 0.8028 (mpp80) REVERT: D 704 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6630 (pt0) outliers start: 92 outliers final: 51 residues processed: 271 average time/residue: 1.0542 time to fit residues: 335.0693 Evaluate side-chains 232 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 173 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 LEU 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 435 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 600 ILE 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 219 ASP Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 600 ILE 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 123 LEU 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 282 LEU Chi-restraints excluded: chain C residue 289 GLN 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 540 LEU Chi-restraints excluded: chain C residue 600 ILE 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 153 THR 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 483 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 702 VAL 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 196 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 678 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1899 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= 0.161 Angle : 0.587 14.938 27812 Z= 0.288 Chirality : 0.041 0.478 3140 Planarity : 0.004 0.065 3432 Dihedral : 4.109 39.388 2704 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 4.14 % Allowed : 14.66 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2432 helix: 2.34 (0.14), residues: 1452 sheet: -1.21 (0.43), residues: 112 loop : -2.19 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 173 HIS 0.008 0.001 HIS D 516 PHE 0.011 0.001 PHE C 525 TYR 0.011 0.001 TYR D 93 ARG 0.004 0.000 ARG C 275 *********************** 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 291 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 201 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7792 (pp) REVERT: A 704 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.5850 (pp20) REVERT: B 123 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7812 (pp) REVERT: B 704 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.5918 (pp20) REVERT: C 123 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (pp) REVERT: C 704 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.5816 (pp20) REVERT: D 123 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7767 (pp) REVERT: D 704 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.5879 (pp20) outliers start: 90 outliers final: 47 residues processed: 268 average time/residue: 1.0099 time to fit residues: 314.4242 Evaluate side-chains 240 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 185 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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 136 GLN 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 436 ILE 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 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 153 THR 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 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 436 ILE 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 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 483 VAL 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 702 VAL 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 79 optimal weight: 0.0070 chunk 212 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: