Starting phenix.real_space_refine on Tue Nov 19 18:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/11_2024/8ekr_28211.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/11_2024/8ekr_28211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/11_2024/8ekr_28211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/11_2024/8ekr_28211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/11_2024/8ekr_28211.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/11_2024/8ekr_28211.cif" } resolution = 3.0 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= 1.000 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 C 12940 2.51 5 N 3288 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 12.26, per 1000 atoms: 0.62 Number of scatterers: 19712 At special positions: 0 Unit cell: (137.97, 137.97, 113.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 4 15.00 O 3368 8.00 N 3288 7.00 C 12940 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: 4.74 Conformation dependent library (CDL) restraints added in 2.4 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 61.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.771A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 471 through 492 removed outlier: 4.046A pdb=" N ALA A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.638A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 619 through 650 removed outlier: 3.568A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.770A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 492 removed outlier: 4.047A pdb=" N ALA B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.638A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 4.072A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.769A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.573A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.246A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 471 through 492 removed outlier: 4.046A pdb=" N ALA C 480 " --> pdb=" O PHE C 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.639A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 519 through 529 removed outlier: 3.616A pdb=" N VAL C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.770A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 471 through 492 removed outlier: 4.047A pdb=" N ALA D 480 " --> pdb=" O PHE D 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.637A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 5.008A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 5.009A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 5.008A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 5.009A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3012 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: 6.00 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2980 1.31 - 1.44: 5712 1.44 - 1.56: 11320 1.56 - 1.69: 8 1.69 - 1.82: 172 Bond restraints: 20192 Sorted by residual: bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX D 801 " pdb=" O4 PEX D 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX B 801 " pdb=" O4 PEX B 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C14 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 27074 3.22 - 6.43: 278 6.43 - 9.65: 36 9.65 - 12.87: 4 12.87 - 16.08: 4 Bond angle restraints: 27396 Sorted by residual: angle pdb=" C ASN B 259 " pdb=" N SER B 260 " pdb=" CA SER B 260 " ideal model delta sigma weight residual 120.49 129.47 -8.98 1.42e+00 4.96e-01 4.00e+01 angle pdb=" C ASN A 259 " pdb=" N SER A 260 " pdb=" CA SER A 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN D 259 " pdb=" N SER D 260 " pdb=" CA SER D 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN C 259 " pdb=" N SER C 260 " pdb=" CA SER C 260 " ideal model delta sigma weight residual 120.49 129.42 -8.93 1.42e+00 4.96e-01 3.95e+01 angle pdb=" O3 PEX D 801 " pdb=" P1 PEX D 801 " pdb=" O8 PEX D 801 " ideal model delta sigma weight residual 93.74 109.82 -16.08 3.00e+00 1.11e-01 2.87e+01 ... (remaining 27391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 10940 18.88 - 37.76: 768 37.76 - 56.65: 108 56.65 - 75.53: 44 75.53 - 94.41: 16 Dihedral angle restraints: 11876 sinusoidal: 4712 harmonic: 7164 Sorted by residual: dihedral pdb=" CA PHE D 161 " pdb=" C PHE D 161 " pdb=" N TYR D 162 " pdb=" CA TYR D 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE C 161 " pdb=" C PHE C 161 " pdb=" N TYR C 162 " pdb=" CA TYR C 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 161 " pdb=" C PHE B 161 " pdb=" N TYR B 162 " pdb=" CA TYR B 162 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2076 0.036 - 0.072: 760 0.072 - 0.107: 221 0.107 - 0.143: 52 0.143 - 0.179: 23 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 3129 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 725 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO D 726 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 726 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 726 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO C 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.044 5.00e-02 4.00e+02 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5451 2.81 - 3.33: 18085 3.33 - 3.86: 32646 3.86 - 4.38: 36887 4.38 - 4.90: 64293 Nonbonded interactions: 157362 Sorted by model distance: nonbonded pdb=" O LEU B 513 " pdb=" OG1 THR B 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU A 513 " pdb=" OG1 THR A 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU C 513 " pdb=" OG1 THR C 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.293 3.040 nonbonded pdb=" O TRP C 223 " pdb=" OG1 THR C 227 " model vdw 2.304 3.040 ... (remaining 157357 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: 3.770 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.980 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.004 0.074 20192 Z= 0.229 Angle : 0.804 16.085 27396 Z= 0.390 Chirality : 0.043 0.179 3132 Planarity : 0.006 0.081 3352 Dihedral : 14.011 94.410 7244 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.38 % Allowed : 0.57 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.13 (0.15), residues: 2412 helix: -0.08 (0.13), residues: 1368 sheet: -0.04 (0.43), residues: 108 loop : -1.79 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS D 169 PHE 0.015 0.001 PHE D 75 TYR 0.034 0.002 TYR D 162 ARG 0.010 0.001 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 481 time to evaluate : 2.147 Fit side-chains REVERT: A 123 LYS cc_start: 0.8090 (tptm) cc_final: 0.7870 (tptm) REVERT: A 189 ASP cc_start: 0.7587 (t0) cc_final: 0.7268 (t0) REVERT: B 123 LYS cc_start: 0.8095 (tptm) cc_final: 0.7876 (tptm) REVERT: B 189 ASP cc_start: 0.7591 (t0) cc_final: 0.7268 (t0) REVERT: C 123 LYS cc_start: 0.8092 (tptm) cc_final: 0.7862 (tptm) REVERT: C 189 ASP cc_start: 0.7582 (t0) cc_final: 0.7267 (t0) REVERT: D 123 LYS cc_start: 0.8085 (tptm) cc_final: 0.7861 (tptm) REVERT: D 189 ASP cc_start: 0.7592 (t0) cc_final: 0.7271 (t0) outliers start: 8 outliers final: 0 residues processed: 489 average time/residue: 1.1080 time to fit residues: 623.0223 Evaluate side-chains 347 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.0020 chunk 221 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 247 ASN B 148 ASN B 156 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 487 GLN C 148 ASN C 156 GLN C 247 ASN C 487 GLN D 148 ASN D 156 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20192 Z= 0.158 Angle : 0.524 9.222 27396 Z= 0.261 Chirality : 0.037 0.168 3132 Planarity : 0.004 0.058 3352 Dihedral : 6.452 84.031 2784 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.97 % Allowed : 11.16 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.30 (0.16), residues: 2412 helix: 1.14 (0.13), residues: 1456 sheet: 2.55 (0.50), residues: 68 loop : -1.63 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 333 HIS 0.004 0.001 HIS D 521 PHE 0.009 0.001 PHE D 75 TYR 0.027 0.001 TYR B 162 ARG 0.006 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7730 (t0) cc_final: 0.7484 (t0) REVERT: A 371 ARG cc_start: 0.7822 (mmt90) cc_final: 0.7050 (mmp-170) REVERT: A 388 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7221 (tpp-160) REVERT: A 433 MET cc_start: 0.7719 (tpt) cc_final: 0.7373 (tpp) REVERT: A 468 MET cc_start: 0.6306 (ppp) cc_final: 0.5935 (tmm) REVERT: A 520 GLN cc_start: 0.6766 (pm20) cc_final: 0.6487 (pm20) REVERT: A 637 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (mt) REVERT: A 640 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8022 (ttp) REVERT: B 123 LYS cc_start: 0.7972 (tptm) cc_final: 0.7607 (tptm) REVERT: B 189 ASP cc_start: 0.7732 (t0) cc_final: 0.7455 (t0) REVERT: B 371 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7050 (mmp-170) REVERT: B 388 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7212 (tpp-160) REVERT: B 538 LEU cc_start: 0.8140 (mm) cc_final: 0.7871 (mm) REVERT: B 637 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 640 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8019 (ttp) REVERT: B 708 GLU cc_start: 0.8348 (tt0) cc_final: 0.8147 (mt-10) REVERT: C 189 ASP cc_start: 0.7708 (t0) cc_final: 0.7461 (t0) REVERT: C 371 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7051 (mmp-170) REVERT: C 388 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7215 (tpp-160) REVERT: C 468 MET cc_start: 0.6993 (tmm) cc_final: 0.6695 (tmm) REVERT: C 538 LEU cc_start: 0.8146 (mm) cc_final: 0.7881 (mm) REVERT: C 637 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 640 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8018 (ttp) REVERT: C 708 GLU cc_start: 0.8349 (tt0) cc_final: 0.8115 (mt-10) REVERT: D 123 LYS cc_start: 0.7974 (tptm) cc_final: 0.7617 (tptm) REVERT: D 189 ASP cc_start: 0.7712 (t0) cc_final: 0.7440 (t0) REVERT: D 371 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7050 (mmp-170) REVERT: D 388 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7209 (tpp-160) REVERT: D 468 MET cc_start: 0.6986 (tmm) cc_final: 0.6669 (tmm) REVERT: D 538 LEU cc_start: 0.8130 (mm) cc_final: 0.7861 (mm) REVERT: D 637 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8521 (mt) REVERT: D 640 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8025 (ttp) outliers start: 62 outliers final: 36 residues processed: 369 average time/residue: 0.9324 time to fit residues: 397.5353 Evaluate side-chains 374 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 326 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 0.0030 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.5128 ------------------------------------------------------------------------------- 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: