Starting phenix.real_space_refine on Tue Oct 15 06:29:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/10_2024/7xeo_33157.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/10_2024/7xeo_33157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/10_2024/7xeo_33157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/10_2024/7xeo_33157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/10_2024/7xeo_33157.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeo_33157/10_2024/7xeo_33157.cif" } resolution = 2.89 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 13064 2.51 5 N 3372 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Restraints were copied for chains: C, B, D Time building chain proxies: 10.18, per 1000 atoms: 0.51 Number of scatterers: 19980 At special positions: 0 Unit cell: (157.17, 157.17, 117.624, 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 3436 8.00 N 3372 7.00 C 13064 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: 4.72 Conformation dependent library (CDL) restraints added in 2.5 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: 116 helices and 4 sheets defined 63.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 96 removed outlier: 4.070A pdb=" N LEU A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.539A pdb=" N ASP A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.566A pdb=" N VAL A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.551A pdb=" N TYR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.523A pdb=" N ARG A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) 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 363 through 368 removed outlier: 3.745A pdb=" N ARG A 366 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 368 " --> pdb=" O HIS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 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: 3.842A 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 488 removed outlier: 3.975A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.568A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 514 through 531 removed outlier: 4.150A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.553A pdb=" N SER A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 630 removed outlier: 3.522A pdb=" N LEU A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 668 removed outlier: 3.804A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.699A pdb=" N TRP A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 86 through 96 removed outlier: 4.070A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.539A pdb=" N ASP B 140 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 182 removed outlier: 3.567A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.500A pdb=" N VAL B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 removed outlier: 3.523A pdb=" N ARG B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) 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 363 through 368 removed outlier: 3.746A pdb=" N ARG B 366 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 368 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 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: 3.842A 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 488 removed outlier: 3.975A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.567A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 510 Processing helix chain 'B' and resid 514 through 531 removed outlier: 4.150A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 601 removed outlier: 3.552A pdb=" N SER B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 removed outlier: 3.522A pdb=" N LEU B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 668 removed outlier: 3.803A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.699A pdb=" N TRP B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 86 through 96 removed outlier: 4.069A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 130 through 142 removed outlier: 3.539A pdb=" N ASP C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 removed outlier: 3.566A pdb=" N VAL C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.551A pdb=" N TYR C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.522A pdb=" N ARG C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) 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 363 through 368 removed outlier: 3.744A pdb=" N ARG C 366 " --> pdb=" O HIS C 363 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 368 " --> pdb=" O HIS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 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: 3.842A 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 488 removed outlier: 3.976A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.568A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 510 Processing helix chain 'C' and resid 514 through 531 removed outlier: 4.151A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 601 removed outlier: 3.552A pdb=" N SER C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 630 removed outlier: 3.521A pdb=" N LEU C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN C 645 " --> pdb=" O SER C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 668 removed outlier: 3.804A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.700A pdb=" N TRP C 710 " --> pdb=" O ASN C 706 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 712 " --> pdb=" O ALA C 708 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.554A pdb=" N LEU D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 96 removed outlier: 4.070A pdb=" N LEU D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.538A pdb=" N ASP D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.609A pdb=" N ILE D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.567A pdb=" N VAL D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.552A pdb=" N TYR D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 removed outlier: 3.523A pdb=" N ARG D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) 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 363 through 368 removed outlier: 3.745A pdb=" N ARG D 366 " --> pdb=" O HIS D 363 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 368 " --> pdb=" O HIS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 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: 3.843A 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 488 removed outlier: 3.976A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 506 removed outlier: 3.568A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 510 Processing helix chain 'D' and resid 514 through 531 removed outlier: 4.150A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 removed outlier: 3.529A pdb=" N ALA D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 601 removed outlier: 3.552A pdb=" N SER D 592 " --> pdb=" O ILE D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 630 removed outlier: 3.522A pdb=" N LEU D 627 " --> pdb=" O ALA D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 648 removed outlier: 3.523A pdb=" N ASN D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 668 removed outlier: 3.804A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.699A pdb=" N TRP D 710 " --> pdb=" O ASN D 706 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 712 " --> pdb=" O ALA D 708 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 684 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 684 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 684 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 333 through 339 removed outlier: 4.094A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 684 " --> pdb=" O ARG D 697 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 3045 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: 5.38 Time building geometry restraints manager: 5.45 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: 6019 1.34 - 1.46: 3242 1.46 - 1.57: 11063 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 20484 Sorted by residual: bond pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.58e-02 4.01e+03 6.34e+00 bond pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.58e-02 4.01e+03 6.25e+00 bond pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.58e-02 4.01e+03 6.10e+00 bond pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.58e-02 4.01e+03 5.94e+00 bond pdb=" CA GLU C 371 " pdb=" C GLU C 371 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.26e-02 6.30e+03 5.02e+00 ... (remaining 20479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 27229 2.06 - 4.11: 480 4.11 - 6.17: 71 6.17 - 8.22: 8 8.22 - 10.28: 8 Bond angle restraints: 27796 Sorted by residual: angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N VAL B 148 " pdb=" CA VAL B 148 " pdb=" C VAL B 148 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N VAL C 148 " pdb=" CA VAL C 148 " pdb=" C VAL C 148 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N VAL D 148 " pdb=" CA VAL D 148 " pdb=" C VAL D 148 " ideal model delta sigma weight residual 113.53 108.79 4.74 9.80e-01 1.04e+00 2.34e+01 angle pdb=" N LEU B 532 " pdb=" CA LEU B 532 " pdb=" C LEU B 532 " ideal model delta sigma weight residual 114.75 108.88 5.87 1.26e+00 6.30e-01 2.17e+01 ... (remaining 27791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 10948 17.21 - 34.43: 887 34.43 - 51.64: 153 51.64 - 68.85: 16 68.85 - 86.07: 20 Dihedral angle restraints: 12024 sinusoidal: 4856 harmonic: 7168 Sorted by residual: dihedral pdb=" N GLU A 371 " pdb=" C GLU A 371 " pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta harmonic sigma weight residual 122.80 138.19 -15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" N GLU B 371 " pdb=" C GLU B 371 " pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta harmonic sigma weight residual 122.80 138.17 -15.37 0 2.50e+00 1.60e-01 3.78e+01 dihedral pdb=" N GLU C 371 " pdb=" C GLU C 371 " pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta harmonic sigma weight residual 122.80 138.15 -15.35 0 2.50e+00 1.60e-01 3.77e+01 ... (remaining 12021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3123 0.140 - 0.280: 13 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA GLU A 371 " pdb=" N GLU A 371 " pdb=" C GLU A 371 " pdb=" CB GLU A 371 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA GLU C 371 " pdb=" N GLU C 371 " pdb=" C GLU C 371 " pdb=" CB GLU C 371 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA GLU B 371 " pdb=" N GLU B 371 " pdb=" C GLU B 371 " pdb=" CB GLU B 371 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 3137 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 70 " 0.019 2.00e-02 2.50e+03 1.82e-02 5.78e+00 pdb=" CG PHE C 70 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 70 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 70 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 70 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 70 " -0.019 2.00e-02 2.50e+03 1.82e-02 5.78e+00 pdb=" CG PHE B 70 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 70 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 70 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 70 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 70 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " 0.019 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE D 70 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.000 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2311 2.75 - 3.29: 20093 3.29 - 3.83: 33115 3.83 - 4.36: 37144 4.36 - 4.90: 65414 Nonbonded interactions: 158077 Sorted by model distance: nonbonded pdb=" OD1 ASN A 143 " pdb=" CD PRO A 144 " model vdw 2.214 3.440 nonbonded pdb=" OD1 ASN C 143 " pdb=" CD PRO C 144 " model vdw 2.214 3.440 nonbonded pdb=" OD1 ASN B 143 " pdb=" CD PRO B 144 " model vdw 2.214 3.440 nonbonded pdb=" OD1 ASN D 143 " pdb=" CD PRO D 144 " model vdw 2.215 3.440 nonbonded pdb=" N GLN C 145 " pdb=" OE1 GLN C 145 " model vdw 2.252 3.120 ... (remaining 158072 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 40.360 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 0.040 20484 Z= 0.174 Angle : 0.698 10.281 27796 Z= 0.412 Chirality : 0.046 0.700 3140 Planarity : 0.003 0.031 3432 Dihedral : 12.941 86.069 7400 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.99 % Allowed : 4.28 % Favored : 94.74 % Rotamer: Outliers : 0.74 % Allowed : 0.37 % Favored : 98.90 % Cbeta Deviations : 0.17 % 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: 0.03 (0.18), residues: 2432 helix: 1.74 (0.14), residues: 1444 sheet: -4.18 (0.42), residues: 84 loop : -2.56 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 652 HIS 0.005 0.001 HIS B 516 PHE 0.042 0.001 PHE B 70 TYR 0.010 0.001 TYR C 93 ARG 0.003 0.000 ARG D 485 *********************** 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 301 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7983 (tp40) REVERT: A 272 MET cc_start: 0.8626 (tpp) cc_final: 0.8407 (tpp) REVERT: B 539 TYR cc_start: 0.8375 (t80) cc_final: 0.8035 (t80) REVERT: C 70 PHE cc_start: 0.2820 (m-80) cc_final: 0.2450 (m-10) REVERT: C 188 ARG cc_start: 0.7369 (mmt90) cc_final: 0.6861 (mmt90) REVERT: D 76 PHE cc_start: 0.8075 (m-10) cc_final: 0.7854 (m-80) REVERT: D 539 TYR cc_start: 0.8394 (t80) cc_final: 0.8052 (t80) outliers start: 16 outliers final: 8 residues processed: 300 average time/residue: 1.2632 time to fit residues: 430.0689 Evaluate side-chains 200 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 0.0770 chunk 63 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20484 Z= 0.204 Angle : 0.628 9.893 27796 Z= 0.316 Chirality : 0.041 0.238 3140 Planarity : 0.004 0.039 3432 Dihedral : 6.090 105.178 2716 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.65 % Rotamer: Outliers : 2.39 % Allowed : 11.44 % Favored : 86.17 % 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: 0.40 (0.18), residues: 2432 helix: 2.02 (0.14), residues: 1456 sheet: -3.88 (0.41), residues: 84 loop : -2.45 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 655 HIS 0.007 0.001 HIS D 516 PHE 0.032 0.001 PHE A 70 TYR 0.018 0.001 TYR B 223 ARG 0.007 0.000 ARG C 95 *********************** 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 252 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7944 (tp40) REVERT: C 188 ARG cc_start: 0.7449 (mmt90) cc_final: 0.7209 (mmt90) REVERT: C 409 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: C 431 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8447 (tm) REVERT: D 188 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7175 (mmt90) REVERT: D 635 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7873 (ttt) outliers start: 52 outliers final: 18 residues processed: 231 average time/residue: 1.0196 time to fit residues: 276.6336 Evaluate side-chains 191 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 635 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 221 optimal weight: 10.0000 chunk 239 optimal weight: 0.5980 chunk 197 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 525 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 525 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20484 Z= 0.318 Angle : 0.626 8.110 27796 Z= 0.318 Chirality : 0.041 0.218 3140 Planarity : 0.004 0.060 3432 Dihedral : 4.066 33.390 2698 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.96 % Favored : 93.71 % Rotamer: Outliers : 3.17 % Allowed : 13.83 % Favored : 83.00 % 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: 0.64 (0.18), residues: 2432 helix: 2.32 (0.14), residues: 1400 sheet: -3.88 (0.40), residues: 84 loop : -2.26 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 698 HIS 0.005 0.001 HIS D 516 PHE 0.026 0.002 PHE B 70 TYR 0.010 0.001 TYR C 510 ARG 0.004 0.000 ARG C 95 *********************** 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 232 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 163 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7961 (tp40) REVERT: A 370 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 431 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8647 (tt) REVERT: B 370 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7829 (pp) REVERT: C 70 PHE cc_start: 0.3256 (m-80) cc_final: 0.2991 (m-10) REVERT: C 121 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8811 (mt) REVERT: C 370 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7813 (pp) REVERT: C 431 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8530 (tm) REVERT: C 486 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: D 76 PHE cc_start: 0.8094 (m-10) cc_final: 0.7863 (m-80) REVERT: D 370 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7824 (pp) outliers start: 69 outliers final: 26 residues processed: 205 average time/residue: 1.0687 time to fit residues: 257.2251 Evaluate side-chains 184 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 626 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.0770 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20484 Z= 0.152 Angle : 0.562 13.987 27796 Z= 0.278 Chirality : 0.038 0.166 3140 Planarity : 0.004 0.068 3432 Dihedral : 3.797 27.236 2696 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.18 % Favored : 94.49 % Rotamer: Outliers : 3.45 % Allowed : 15.17 % Favored : 81.39 % 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: 0.95 (0.18), residues: 2432 helix: 2.59 (0.14), residues: 1400 sheet: -3.55 (0.42), residues: 84 loop : -2.18 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 173 HIS 0.005 0.001 HIS D 516 PHE 0.020 0.001 PHE B 70 TYR 0.008 0.001 TYR B 223 ARG 0.004 0.000 ARG D 72 *********************** 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 241 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 166 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7560 (t0) REVERT: A 230 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7915 (tp40) REVERT: A 370 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7434 (pp) REVERT: A 486 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: B 370 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7433 (pp) REVERT: B 486 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: C 70 PHE cc_start: 0.3354 (m-80) cc_final: 0.3018 (m-10) REVERT: C 99 LYS cc_start: 0.6501 (ptpt) cc_final: 0.5987 (pttp) REVERT: C 121 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8699 (mt) REVERT: C 188 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7195 (mmt90) REVERT: C 370 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7458 (pp) REVERT: C 431 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8502 (tm) REVERT: C 486 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: D 76 PHE cc_start: 0.8082 (m-10) cc_final: 0.7834 (m-80) REVERT: D 370 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7427 (pp) REVERT: D 431 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8618 (tt) REVERT: D 486 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8131 (m-80) outliers start: 75 outliers final: 24 residues processed: 219 average time/residue: 1.1286 time to fit residues: 285.7483 Evaluate side-chains 188 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 486 PHE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 201 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 515 GLN B 668 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 GLN D 515 GLN D 668 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2121 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: