Starting phenix.real_space_refine on Sun Aug 24 02:52:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxf_37905/08_2025/8wxf_37905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxf_37905/08_2025/8wxf_37905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2025/8wxf_37905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2025/8wxf_37905.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2025/8wxf_37905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2025/8wxf_37905.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 48 5.16 5 C 10302 2.51 5 N 2820 2.21 5 O 3210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16380 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "B" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "C" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Time building chain proxies: 3.25, per 1000 atoms: 0.20 Number of scatterers: 16380 At special positions: 0 Unit cell: (116.16, 113.52, 146.96, 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 48 16.00 O 3210 8.00 N 2820 7.00 C 10302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 502.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 21 sheets defined 34.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.645A pdb=" N ALA A 81 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.099A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 293 removed outlier: 4.055A pdb=" N ALA A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.500A pdb=" N GLY A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.220A pdb=" N THR A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 617 through 626 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.917A pdb=" N ALA B 82 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 225 through 254 Proline residue: B 238 - end of helix removed outlier: 3.673A pdb=" N ALA B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 292 removed outlier: 4.024A pdb=" N ALA B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 314 Processing helix chain 'B' and resid 321 through 343 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.540A pdb=" N GLY B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 606 through 611 removed outlier: 4.488A pdb=" N VAL B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 643 through 659 removed outlier: 3.753A pdb=" N ASN B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.617A pdb=" N ALA C 81 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 82 " --> pdb=" O MET C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 139 through 153 Processing helix chain 'C' and resid 178 through 185 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 225 through 254 Proline residue: C 238 - end of helix Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.528A pdb=" N ILE C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.041A pdb=" N ASP C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.640A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.550A pdb=" N ILE C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.646A pdb=" N GLY C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.539A pdb=" N ILE C 607 " --> pdb=" O PRO C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 694 through 699 removed outlier: 4.555A pdb=" N GLY C 699 " --> pdb=" O ILE C 695 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.777A pdb=" N ILE A 17 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 25 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 52 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET A 51 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 124 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 125 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.615A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.921A pdb=" N GLN A 380 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 457 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET A 408 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 460 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 410 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA A 462 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.800A pdb=" N ALA A 539 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.869A pdb=" N LEU A 499 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.344A pdb=" N MET B 51 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 124 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 125 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.997A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 381 through 388 removed outlier: 6.721A pdb=" N MET B 408 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER B 460 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 498 through 499 Processing sheet with id=AB4, first strand: chain 'B' and resid 539 through 540 removed outlier: 6.834A pdb=" N ALA B 539 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 25 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 17 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 30 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 52 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 124 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 125 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 175 removed outlier: 6.718A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 380 through 388 removed outlier: 6.174A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 408 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER C 460 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 500 removed outlier: 3.764A pdb=" N VAL C 519 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 539 through 540 removed outlier: 6.870A pdb=" N ALA C 539 " --> pdb=" O THR C 546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 removed outlier: 3.633A pdb=" N PHE C 638 " --> pdb=" O SER C 630 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 723 through 724 removed outlier: 4.114A pdb=" N ASP C 723 " --> pdb=" O SER C 731 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 731 " --> pdb=" O ASP C 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 657 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5634 1.34 - 1.46: 3225 1.46 - 1.58: 7680 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 16626 Sorted by residual: bond pdb=" N VAL B 278 " pdb=" CA VAL B 278 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" N GLU C 77 " pdb=" CA GLU C 77 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.52e+00 bond pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.23e-02 6.61e+03 6.52e+00 bond pdb=" N LEU C 313 " pdb=" CA LEU C 313 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.17e+00 bond pdb=" N MET C 497 " pdb=" CA MET C 497 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.07e+00 ... (remaining 16621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22045 2.05 - 4.10: 436 4.10 - 6.15: 64 6.15 - 8.20: 14 8.20 - 10.25: 7 Bond angle restraints: 22566 Sorted by residual: angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 113.47 108.80 4.67 1.01e+00 9.80e-01 2.14e+01 angle pdb=" N VAL A 510 " pdb=" CA VAL A 510 " pdb=" C VAL A 510 " ideal model delta sigma weight residual 113.71 109.59 4.12 9.50e-01 1.11e+00 1.88e+01 angle pdb=" N ASP C 47 " pdb=" CA ASP C 47 " pdb=" C ASP C 47 " ideal model delta sigma weight residual 112.86 107.89 4.97 1.22e+00 6.72e-01 1.66e+01 angle pdb=" CA GLU A 515 " pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLN A 311 " pdb=" CB GLN A 311 " pdb=" CG GLN A 311 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.37e+01 ... (remaining 22561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8590 17.48 - 34.97: 1139 34.97 - 52.45: 290 52.45 - 69.93: 51 69.93 - 87.42: 34 Dihedral angle restraints: 10104 sinusoidal: 3918 harmonic: 6186 Sorted by residual: dihedral pdb=" CA GLU B 515 " pdb=" C GLU B 515 " pdb=" N ARG B 516 " pdb=" CA ARG B 516 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 554 " pdb=" C LEU A 554 " pdb=" N ASP A 555 " pdb=" CA ASP A 555 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 524 " pdb=" C ILE B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1995 0.047 - 0.095: 502 0.095 - 0.142: 169 0.142 - 0.189: 8 0.189 - 0.236: 2 Chirality restraints: 2676 Sorted by residual: chirality pdb=" CB VAL B 561 " pdb=" CA VAL B 561 " pdb=" CG1 VAL B 561 " pdb=" CG2 VAL B 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL A 561 " pdb=" CA VAL A 561 " pdb=" CG1 VAL A 561 " pdb=" CG2 VAL A 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2673 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 557 " 0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 558 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 558 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 558 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 267 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 268 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 47 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" CG ASP B 47 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP B 47 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP B 47 " 0.019 2.00e-02 2.50e+03 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1107 2.73 - 3.27: 17011 3.27 - 3.82: 25895 3.82 - 4.36: 28346 4.36 - 4.90: 48783 Nonbonded interactions: 121142 Sorted by model distance: nonbonded pdb=" O ASP A 343 " pdb=" ND1 HIS A 344 " model vdw 2.188 3.120 nonbonded pdb=" O ASN A 655 " pdb=" NE2 GLN A 661 " model vdw 2.224 3.120 nonbonded pdb=" O ALA B 287 " pdb=" OG1 THR B 291 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG C 356 " pdb=" OD2 ASP C 523 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG C 350 " pdb=" O GLY C 351 " model vdw 2.243 3.120 ... (remaining 121137 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.230 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 0.045 16626 Z= 0.164 Angle : 0.709 10.247 22566 Z= 0.386 Chirality : 0.046 0.236 2676 Planarity : 0.005 0.087 2979 Dihedral : 17.293 87.415 6138 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 0.75 % Allowed : 33.16 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.18), residues: 2184 helix: 0.61 (0.20), residues: 693 sheet: -1.44 (0.31), residues: 325 loop : -1.55 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 406 TYR 0.010 0.001 TYR B 276 PHE 0.014 0.001 PHE C 531 TRP 0.003 0.001 TRP A 173 HIS 0.003 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00325 (16626) covalent geometry : angle 0.70893 (22566) hydrogen bonds : bond 0.17475 ( 654) hydrogen bonds : angle 6.96870 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASP cc_start: 0.9054 (m-30) cc_final: 0.8764 (p0) REVERT: A 333 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8944 (tttt) REVERT: A 337 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8662 (mtp85) REVERT: B 328 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9277 (mt) REVERT: C 208 GLU cc_start: 0.6663 (tp30) cc_final: 0.6335 (tp30) REVERT: C 249 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 482 LEU cc_start: 0.8746 (mm) cc_final: 0.8314 (mm) REVERT: C 495 ILE cc_start: 0.8605 (mp) cc_final: 0.8190 (mm) REVERT: C 534 MET cc_start: 0.7696 (tpt) cc_final: 0.7452 (tpp) outliers start: 13 outliers final: 4 residues processed: 199 average time/residue: 0.0986 time to fit residues: 31.0590 Evaluate side-chains 184 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106183 restraints weight = 31512.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104953 restraints weight = 22400.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106176 restraints weight = 17939.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106564 restraints weight = 14975.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106871 restraints weight = 13001.176| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16626 Z= 0.168 Angle : 0.618 9.700 22566 Z= 0.320 Chirality : 0.045 0.216 2676 Planarity : 0.005 0.059 2979 Dihedral : 4.785 55.781 2357 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % Rotamer: Outliers : 5.07 % Allowed : 28.09 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 2184 helix: 0.84 (0.20), residues: 699 sheet: -1.31 (0.30), residues: 329 loop : -1.43 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.012 0.002 TYR B 270 PHE 0.018 0.001 PHE A 531 TRP 0.006 0.001 TRP C 173 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00386 (16626) covalent geometry : angle 0.61778 (22566) hydrogen bonds : bond 0.04005 ( 654) hydrogen bonds : angle 5.39692 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 182 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7617 (tp30) cc_final: 0.7408 (tp30) REVERT: A 345 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8547 (p90) REVERT: A 442 LEU cc_start: 0.8805 (tp) cc_final: 0.8587 (tp) REVERT: A 482 LEU cc_start: 0.9102 (mm) cc_final: 0.8637 (mm) REVERT: A 522 THR cc_start: 0.9305 (m) cc_final: 0.8819 (p) REVERT: B 389 MET cc_start: 0.8186 (mmm) cc_final: 0.7977 (mtt) REVERT: C 50 ASN cc_start: 0.8489 (m-40) cc_final: 0.8252 (m-40) REVERT: C 215 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8651 (pp20) REVERT: C 482 LEU cc_start: 0.8749 (mm) cc_final: 0.8234 (mm) outliers start: 88 outliers final: 48 residues processed: 248 average time/residue: 0.1019 time to fit residues: 41.1341 Evaluate side-chains 211 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 145 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101197 restraints weight = 31268.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104148 restraints weight = 18011.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106142 restraints weight = 12604.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107368 restraints weight = 10045.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108199 restraints weight = 8762.958| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16626 Z= 0.168 Angle : 0.599 11.551 22566 Z= 0.307 Chirality : 0.044 0.204 2676 Planarity : 0.005 0.057 2979 Dihedral : 4.546 54.153 2355 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 5.31 % Allowed : 28.09 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.18), residues: 2184 helix: 0.98 (0.20), residues: 702 sheet: -1.32 (0.29), residues: 329 loop : -1.34 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 406 TYR 0.019 0.002 TYR A 276 PHE 0.022 0.001 PHE B 345 TRP 0.006 0.001 TRP C 173 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00390 (16626) covalent geometry : angle 0.59940 (22566) hydrogen bonds : bond 0.03885 ( 654) hydrogen bonds : angle 5.12465 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 165 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.8798 (tp) cc_final: 0.8578 (tp) REVERT: A 522 THR cc_start: 0.9226 (m) cc_final: 0.8743 (p) REVERT: B 389 MET cc_start: 0.8231 (mmm) cc_final: 0.8014 (mtt) REVERT: C 30 GLU cc_start: 0.8172 (tt0) cc_final: 0.7740 (mt-10) REVERT: C 215 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: C 249 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 320 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7206 (mtm-85) REVERT: C 497 MET cc_start: 0.8137 (mmt) cc_final: 0.7911 (mmm) outliers start: 92 outliers final: 56 residues processed: 233 average time/residue: 0.0949 time to fit residues: 35.9428 Evaluate side-chains 223 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102835 restraints weight = 31611.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101589 restraints weight = 22860.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102112 restraints weight = 19129.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102712 restraints weight = 16087.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103037 restraints weight = 13846.011| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16626 Z= 0.237 Angle : 0.647 11.992 22566 Z= 0.331 Chirality : 0.046 0.325 2676 Planarity : 0.005 0.059 2979 Dihedral : 4.704 54.778 2355 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.46 % Favored : 93.41 % Rotamer: Outliers : 6.29 % Allowed : 28.09 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.18), residues: 2184 helix: 0.90 (0.20), residues: 708 sheet: -1.36 (0.29), residues: 312 loop : -1.41 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 339 TYR 0.015 0.002 TYR A 80 PHE 0.027 0.002 PHE A 345 TRP 0.004 0.001 TRP C 173 HIS 0.004 0.001 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00542 (16626) covalent geometry : angle 0.64658 (22566) hydrogen bonds : bond 0.04035 ( 654) hydrogen bonds : angle 5.13520 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 161 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8577 (m) REVERT: A 311 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8973 (mm-40) REVERT: A 695 ILE cc_start: 0.1860 (OUTLIER) cc_final: 0.1610 (pt) REVERT: B 412 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8377 (m-40) REVERT: C 30 GLU cc_start: 0.8153 (tt0) cc_final: 0.7755 (mt-10) REVERT: C 50 ASN cc_start: 0.8567 (m-40) cc_final: 0.8263 (m-40) REVERT: C 215 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8733 (pp20) REVERT: C 320 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7151 (mtm-85) REVERT: C 497 MET cc_start: 0.8112 (mmt) cc_final: 0.7827 (mmm) outliers start: 109 outliers final: 75 residues processed: 247 average time/residue: 0.0880 time to fit residues: 35.6394 Evaluate side-chains 235 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 155 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9278 > 50: distance: 33 - 53: 6.522 distance: 37 - 58: 23.729 distance: 46 - 53: 6.874 distance: 53 - 54: 4.594 distance: 54 - 55: 17.308 distance: 54 - 57: 8.356 distance: 55 - 56: 23.011 distance: 55 - 58: 16.223 distance: 58 - 59: 9.891 distance: 59 - 60: 15.317 distance: 59 - 62: 23.033 distance: 60 - 61: 15.061 distance: 60 - 66: 16.783 distance: 62 - 63: 30.534 distance: 62 - 64: 29.163 distance: 63 - 65: 23.308 distance: 66 - 67: 3.004 distance: 67 - 68: 4.324 distance: 67 - 70: 12.471 distance: 68 - 69: 15.427 distance: 68 - 74: 12.045 distance: 70 - 71: 18.778 distance: 71 - 72: 9.961 distance: 71 - 73: 12.088 distance: 74 - 75: 10.018 distance: 75 - 76: 16.198 distance: 75 - 78: 12.621 distance: 76 - 77: 29.812 distance: 76 - 85: 28.982 distance: 78 - 79: 6.622 distance: 79 - 80: 7.958 distance: 80 - 81: 4.009 distance: 81 - 82: 3.943 distance: 82 - 83: 7.285 distance: 82 - 84: 4.843 distance: 85 - 86: 20.555 distance: 85 - 91: 17.084 distance: 86 - 87: 21.639 distance: 86 - 89: 17.167 distance: 87 - 88: 18.063 distance: 87 - 92: 11.995 distance: 89 - 90: 25.989 distance: 90 - 91: 12.650 distance: 92 - 93: 12.208 distance: 93 - 94: 15.963 distance: 93 - 96: 27.632 distance: 94 - 95: 7.628 distance: 94 - 100: 11.969 distance: 96 - 97: 22.267 distance: 97 - 98: 17.286 distance: 97 - 99: 14.075 distance: 100 - 101: 14.133 distance: 101 - 102: 8.358 distance: 102 - 103: 10.429 distance: 102 - 109: 5.569 distance: 104 - 105: 11.484 distance: 105 - 106: 26.292 distance: 106 - 107: 14.078 distance: 106 - 108: 20.935 distance: 109 - 110: 15.650 distance: 110 - 111: 21.402 distance: 110 - 113: 8.784 distance: 111 - 112: 4.351 distance: 111 - 117: 20.881 distance: 113 - 114: 17.105 distance: 114 - 115: 12.789 distance: 115 - 116: 18.448 distance: 117 - 118: 26.945 distance: 118 - 119: 13.648 distance: 118 - 121: 25.408 distance: 119 - 123: 6.466 distance: 121 - 122: 25.840 distance: 123 - 124: 5.175 distance: 124 - 125: 8.289 distance: 125 - 126: 13.615 distance: 125 - 130: 30.850 distance: 128 - 129: 7.464