Starting phenix.real_space_refine on Wed Aug 5 12:20:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zbt_74008/08_2026/9zbt_74008.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zbt_74008/08_2026/9zbt_74008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zbt_74008/08_2026/9zbt_74008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zbt_74008/08_2026/9zbt_74008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zbt_74008/08_2026/9zbt_74008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zbt_74008/08_2026/9zbt_74008.map" } resolution = 3.22 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= 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 77 5.49 5 S 32 5.16 5 C 5829 2.51 5 N 1768 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9594 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "A" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 765 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 765 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "G" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "H" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5756 Classifications: {'peptide': 731} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 687} Chain: "J" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 683 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6410 SG CYS H 445 40.119 62.350 50.094 1.00 50.09 S ATOM 6434 SG CYS H 448 40.397 65.832 48.490 1.00 49.50 S ATOM 6569 SG CYS H 463 43.529 64.021 49.812 1.00 50.46 S ATOM 6595 SG CYS H 466 40.807 65.554 52.085 1.00 53.69 S ATOM 6340 SG CYS H 436 43.723 44.211 42.619 1.00 44.36 S ATOM 6364 SG CYS H 439 40.345 45.638 41.688 1.00 45.66 S ATOM 6676 SG CYS H 476 41.198 44.755 45.398 1.00 49.70 S ATOM 6695 SG CYS H 479 40.367 42.207 42.617 1.00 50.18 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG D 113 " occ=0.74 ... (9 atoms not shown) pdb=" NH2 ARG D 113 " occ=0.74 residue: pdb=" N GLU D 114 " occ=0.84 ... (7 atoms not shown) pdb=" OE2 GLU D 114 " occ=0.84 Time building chain proxies: 1.32, per 1000 atoms: 0.14 Number of scatterers: 9594 At special positions: 0 Unit cell: (94.395, 125.86, 132.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 77 15.00 O 1886 8.00 N 1768 7.00 C 5829 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: 0.77 Conformation dependent library (CDL) restraints added in 293.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 801 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 466 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 448 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 445 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 463 " pdb=" ZN H 802 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 439 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 479 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 436 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 476 " Number of angles added : 12 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 37.3% alpha, 17.2% beta 23 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.715A pdb=" N ALA D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 removed outlier: 4.088A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 132 " --> pdb=" O TRP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 154 Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.555A pdb=" N THR A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 64' Processing helix chain 'B' and resid 56 through 61 removed outlier: 4.082A pdb=" N ALA B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.661A pdb=" N ALA H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 removed outlier: 3.985A pdb=" N GLN H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 128 through 133 Processing helix chain 'H' and resid 135 through 148 Processing helix chain 'H' and resid 153 through 158 removed outlier: 4.065A pdb=" N ALA H 156 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 171 removed outlier: 3.629A pdb=" N LEU H 165 " --> pdb=" O ASN H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 213 Processing helix chain 'H' and resid 229 through 244 removed outlier: 3.868A pdb=" N GLN H 244 " --> pdb=" O ASN H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 269 removed outlier: 3.889A pdb=" N THR H 261 " --> pdb=" O LEU H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 295 Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.887A pdb=" N PHE H 308 " --> pdb=" O SER H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 328 removed outlier: 3.858A pdb=" N TYR H 327 " --> pdb=" O ASP H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 349 Processing helix chain 'H' and resid 360 through 369 Processing helix chain 'H' and resid 380 through 384 removed outlier: 3.559A pdb=" N ALA H 384 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 417 Processing helix chain 'H' and resid 490 through 502 removed outlier: 4.097A pdb=" N ALA H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) Proline residue: H 500 - end of helix Processing helix chain 'H' and resid 511 through 516 Processing helix chain 'H' and resid 519 through 530 Processing helix chain 'H' and resid 539 through 545 removed outlier: 3.645A pdb=" N LYS H 544 " --> pdb=" O MET H 541 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY H 545 " --> pdb=" O LEU H 542 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 585 removed outlier: 3.614A pdb=" N ARG H 584 " --> pdb=" O GLN H 580 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 603 through 612 Processing helix chain 'H' and resid 613 through 628 removed outlier: 3.582A pdb=" N PHE H 617 " --> pdb=" O GLY H 613 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 634 Processing helix chain 'H' and resid 648 through 662 Processing helix chain 'H' and resid 697 through 712 Processing helix chain 'H' and resid 713 through 715 No H-bonds generated for 'chain 'H' and resid 713 through 715' Processing helix chain 'H' and resid 717 through 721 removed outlier: 3.503A pdb=" N LYS H 720 " --> pdb=" O ASP H 717 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 721 " --> pdb=" O SER H 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 717 through 721' Processing sheet with id=AA1, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.828A pdb=" N LYS D 88 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE D 135 " --> pdb=" O LYS D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 11 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 11 current: chain 'A' and resid 25 through 38 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 55 current: chain 'A' and resid 89 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 89 through 99 current: chain 'B' and resid 25 through 39 removed outlier: 3.559A pdb=" N LEU B 31 " --> pdb=" O MET B 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET B 50 " --> pdb=" O LEU B 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 42 through 54 current: chain 'B' and resid 86 through 98 Processing sheet with id=AA3, first strand: chain 'H' and resid 16 through 19 removed outlier: 4.186A pdb=" N SER H 48 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA H 7 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL H 46 " --> pdb=" O ALA H 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'H' and resid 273 through 276 removed outlier: 6.266A pdb=" N GLU H 274 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN H 247 " --> pdb=" O VAL H 316 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N VAL H 318 " --> pdb=" O GLN H 247 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU H 249 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASP H 320 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET H 251 " --> pdb=" O ASP H 320 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ILE H 353 " --> pdb=" O GLY H 315 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE H 317 " --> pdb=" O ILE H 353 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY H 355 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE H 319 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP H 220 " --> pdb=" O LEU H 354 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA H 219 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU H 375 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU H 221 " --> pdb=" O LEU H 375 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU H 377 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA H 223 " --> pdb=" O LEU H 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 388 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 388 through 389 current: chain 'H' and resid 535 through 538 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 535 through 538 current: chain 'H' and resid 593 through 598 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 433 through 436 removed outlier: 3.668A pdb=" N ALA H 433 " --> pdb=" O VAL H 487 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 444 through 445 removed outlier: 3.903A pdb=" N HIS H 450 " --> pdb=" O CYS H 445 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 453 through 455 Processing sheet with id=AB1, first strand: chain 'H' and resid 635 through 643 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 635 through 643 current: chain 'H' and resid 687 through 690 No H-bonds generated for sheet with id=AB1 270 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2904 1.34 - 1.46: 1928 1.46 - 1.58: 4945 1.58 - 1.70: 151 1.70 - 1.81: 45 Bond restraints: 9973 Sorted by residual: bond pdb=" C1' DT G 27 " pdb=" N1 DT G 27 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DT G 23 " pdb=" C2' DT G 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 bond pdb=" C3' DG G 26 " pdb=" O3' DG G 26 " ideal model delta sigma weight residual 1.435 1.473 -0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" C1' DC J 32 " pdb=" N1 DC J 32 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.01e+00 bond pdb=" C3' DC J 39 " pdb=" C2' DC J 39 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.73e+00 ... (remaining 9968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 13318 1.30 - 2.60: 409 2.60 - 3.89: 133 3.89 - 5.19: 12 5.19 - 6.49: 2 Bond angle restraints: 13874 Sorted by residual: angle pdb=" C3' DG G 26 " pdb=" O3' DG G 26 " pdb=" P DT G 27 " ideal model delta sigma weight residual 119.70 125.34 -5.64 1.20e+00 6.94e-01 2.21e+01 angle pdb=" CA ASP H 667 " pdb=" CB ASP H 667 " pdb=" CG ASP H 667 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" N3 DT G 27 " pdb=" C4 DT G 27 " pdb=" O4 DT G 27 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT Z 9 " pdb=" C4 DT Z 9 " pdb=" O4 DT Z 9 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT G 30 " pdb=" C4 DT G 30 " pdb=" O4 DT G 30 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 13869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 5404 33.95 - 67.91: 330 67.91 - 101.86: 16 101.86 - 135.81: 1 135.81 - 169.77: 3 Dihedral angle restraints: 5754 sinusoidal: 2809 harmonic: 2945 Sorted by residual: dihedral pdb=" C4' DT G 27 " pdb=" C3' DT G 27 " pdb=" O3' DT G 27 " pdb=" P DA G 28 " ideal model delta sinusoidal sigma weight residual 220.00 50.23 169.77 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 32 " pdb=" C3' DC J 32 " pdb=" O3' DC J 32 " pdb=" P DT J 33 " ideal model delta sinusoidal sigma weight residual 220.00 52.73 167.27 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT G 23 " pdb=" C3' DT G 23 " pdb=" O3' DT G 23 " pdb=" P DC G 24 " ideal model delta sinusoidal sigma weight residual 220.00 53.65 166.35 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 5751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1032 0.033 - 0.066: 302 0.066 - 0.099: 69 0.099 - 0.132: 111 0.132 - 0.165: 41 Chirality restraints: 1555 Sorted by residual: chirality pdb=" P DT G 27 " pdb=" OP1 DT G 27 " pdb=" OP2 DT G 27 " pdb=" O5' DT G 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.50 -0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" C3' DA J 19 " pdb=" C4' DA J 19 " pdb=" O3' DA J 19 " pdb=" C2' DA J 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" C3' DC J 17 " pdb=" C4' DC J 17 " pdb=" O3' DC J 17 " pdb=" C2' DC J 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1552 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 646 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ASN H 646 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN H 646 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN H 647 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 98 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" CD GLU B 98 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU B 98 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 98 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 20 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 21 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.018 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1660 2.78 - 3.31: 8711 3.31 - 3.84: 15510 3.84 - 4.37: 17739 4.37 - 4.90: 29448 Nonbonded interactions: 73068 Sorted by model distance: nonbonded pdb=" O ASN H 646 " pdb=" OD1 ASN H 646 " model vdw 2.252 3.040 nonbonded pdb=" O PRO H 631 " pdb=" O THR H 634 " model vdw 2.466 3.040 nonbonded pdb=" O CYS H 436 " pdb=" O CYS H 439 " model vdw 2.490 3.040 nonbonded pdb=" OD2 ASP H 68 " pdb=" O GLU H 70 " model vdw 2.500 3.040 nonbonded pdb=" O SER H 184 " pdb=" OG SER H 184 " model vdw 2.506 3.040 ... (remaining 73063 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' } 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=0.74 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 0.047 9981 Z= 0.308 Angle : 0.580 9.839 13886 Z= 0.435 Chirality : 0.048 0.165 1555 Planarity : 0.003 0.037 1528 Dihedral : 18.970 169.765 3844 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 are not related in a simple way. whole: 1.88 (0.28), residues: 1013 helix: 2.53 (0.32), residues: 305 sheet: 1.45 (0.35), residues: 252 loop : 0.30 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 146 TYR 0.004 0.000 TYR H 452 PHE 0.006 0.001 PHE H 574 TRP 0.007 0.001 TRP H 671 HIS 0.001 0.000 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.31 ( 9973) covalent geometry : angle 0.56706 / 0.43 (13874) hydrogen bonds : bond 0.14744 / 9.70 ( 332) hydrogen bonds : angle 5.01779 / 3.53 ( 853) metal coordination : bond 0.00366 / 0.18 ( 8) metal coordination : angle 4.16384 / 2.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: D 91 MET cc_start: 0.5295 (tpp) cc_final: 0.4691 (mpp) REVERT: B 45 GLN cc_start: 0.8386 (mt0) cc_final: 0.8179 (mt0) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.0891 time to fit residues: 25.9542 Evaluate side-chains 149 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS B 59 ASN B 60 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** 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 = 0.3926 r_free = 0.3926 target = 0.136538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098531 restraints weight = 18751.863| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.74 r_work: 0.3122 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9981 Z= 0.142 Angle : 0.607 12.601 13886 Z= 0.322 Chirality : 0.043 0.301 1555 Planarity : 0.004 0.040 1528 Dihedral : 22.506 176.922 1931 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.76 % Allowed : 6.57 % Favored : 91.67 % 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 are not related in a simple way. whole: 2.08 (0.28), residues: 1013 helix: 2.38 (0.31), residues: 301 sheet: 1.59 (0.34), residues: 262 loop : 0.65 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.016 0.001 TYR D 92 PHE 0.014 0.002 PHE B 77 TRP 0.029 0.002 TRP H 671 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9973) covalent geometry : angle 0.58714 / 0.32 (13874) hydrogen bonds : bond 0.04075 / 2.73 ( 332) hydrogen bonds : angle 4.13072 / 2.90 ( 853) metal coordination : bond 0.00496 / 0.26 ( 8) metal coordination : angle 5.28998 / 3.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: D 91 MET cc_start: 0.7504 (tpp) cc_final: 0.6786 (mpp) REVERT: D 98 ASP cc_start: 0.8128 (t0) cc_final: 0.7731 (t0) REVERT: D 100 ASP cc_start: 0.6421 (p0) cc_final: 0.5982 (p0) REVERT: B 45 GLN cc_start: 0.8877 (mt0) cc_final: 0.8551 (mt0) REVERT: B 75 GLN cc_start: 0.8583 (pp30) cc_final: 0.7947 (pp30) REVERT: H 117 TYR cc_start: 0.6060 (p90) cc_final: 0.5615 (p90) REVERT: H 587 ARG cc_start: 0.7710 (ptp-110) cc_final: 0.7426 (ptp-110) REVERT: H 691 ILE cc_start: 0.9059 (mt) cc_final: 0.8855 (tt) outliers start: 15 outliers final: 9 residues processed: 172 average time/residue: 0.0955 time to fit residues: 22.0555 Evaluate side-chains 160 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.134171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096462 restraints weight = 18755.813| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.69 r_work: 0.3087 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9981 Z= 0.138 Angle : 0.558 13.068 13886 Z= 0.300 Chirality : 0.042 0.301 1555 Planarity : 0.004 0.043 1528 Dihedral : 22.674 176.921 1931 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.53 % Allowed : 8.69 % Favored : 89.79 % 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 are not related in a simple way. whole: 1.92 (0.28), residues: 1013 helix: 2.18 (0.30), residues: 307 sheet: 1.58 (0.34), residues: 262 loop : 0.53 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 71 TYR 0.008 0.001 TYR H 452 PHE 0.007 0.001 PHE H 617 TRP 0.019 0.001 TRP H 671 HIS 0.006 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 9973) covalent geometry : angle 0.53377 / 0.30 (13874) hydrogen bonds : bond 0.03743 / 2.48 ( 332) hydrogen bonds : angle 3.87653 / 2.72 ( 853) metal coordination : bond 0.00562 / 0.32 ( 8) metal coordination : angle 5.56995 / 3.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 91 MET cc_start: 0.7457 (tpp) cc_final: 0.7102 (mpp) REVERT: D 98 ASP cc_start: 0.8178 (t0) cc_final: 0.7943 (t0) REVERT: B 45 GLN cc_start: 0.8915 (mt0) cc_final: 0.8634 (mt0) REVERT: B 75 GLN cc_start: 0.8700 (pp30) cc_final: 0.8111 (pp30) REVERT: B 96 GLN cc_start: 0.8370 (mp10) cc_final: 0.7998 (mp10) REVERT: H 116 TRP cc_start: 0.7588 (m100) cc_final: 0.7146 (m100) REVERT: H 117 TYR cc_start: 0.6151 (p90) cc_final: 0.5727 (p90) REVERT: H 587 ARG cc_start: 0.7693 (ptp-110) cc_final: 0.7403 (ptp-110) outliers start: 13 outliers final: 10 residues processed: 159 average time/residue: 0.0932 time to fit residues: 19.8569 Evaluate side-chains 152 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093832 restraints weight = 18810.626| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.67 r_work: 0.3041 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9981 Z= 0.151 Angle : 0.582 14.415 13886 Z= 0.304 Chirality : 0.043 0.310 1555 Planarity : 0.004 0.046 1528 Dihedral : 22.838 179.224 1931 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.23 % Allowed : 9.74 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.28), residues: 1013 helix: 2.08 (0.30), residues: 307 sheet: 1.48 (0.34), residues: 264 loop : 0.54 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 146 TYR 0.008 0.001 TYR H 452 PHE 0.007 0.001 PHE H 568 TRP 0.017 0.001 TRP H 671 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 9973) covalent geometry : angle 0.55208 / 0.30 (13874) hydrogen bonds : bond 0.03592 / 2.39 ( 332) hydrogen bonds : angle 3.80233 / 2.67 ( 853) metal coordination : bond 0.00663 / 0.38 ( 8) metal coordination : angle 6.27151 / 3.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: D 91 MET cc_start: 0.7531 (tpp) cc_final: 0.7230 (tpp) REVERT: D 98 ASP cc_start: 0.8369 (t0) cc_final: 0.8083 (t0) REVERT: D 128 TRP cc_start: 0.8328 (m100) cc_final: 0.7818 (m100) REVERT: D 133 LYS cc_start: 0.8153 (tppt) cc_final: 0.7933 (tppt) REVERT: B 45 GLN cc_start: 0.8942 (mt0) cc_final: 0.8654 (mt0) REVERT: B 81 HIS cc_start: 0.6448 (m170) cc_final: 0.6239 (m170) REVERT: H 116 TRP cc_start: 0.7600 (m100) cc_final: 0.7289 (m100) REVERT: H 587 ARG cc_start: 0.7773 (ptp-110) cc_final: 0.7491 (ptp-110) outliers start: 19 outliers final: 14 residues processed: 164 average time/residue: 0.0867 time to fit residues: 19.4636 Evaluate side-chains 157 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 665 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 104 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 HIS H 475 GLN H 483 HIS ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085414 restraints weight = 18691.069| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.71 r_work: 0.2891 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 9981 Z= 0.346 Angle : 0.809 22.814 13886 Z= 0.411 Chirality : 0.050 0.332 1555 Planarity : 0.006 0.070 1528 Dihedral : 23.328 178.280 1931 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.76 % Allowed : 11.03 % Favored : 85.21 % 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 are not related in a simple way. whole: 0.86 (0.26), residues: 1013 helix: 1.25 (0.29), residues: 313 sheet: 0.78 (0.33), residues: 268 loop : 0.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 71 TYR 0.017 0.003 TYR H 335 PHE 0.022 0.002 PHE H 265 TRP 0.048 0.003 TRP H 671 HIS 0.011 0.002 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.35 ( 9973) covalent geometry : angle 0.75011 / 0.41 (13874) hydrogen bonds : bond 0.05878 / 4.02 ( 332) hydrogen bonds : angle 4.33610 / 3.04 ( 853) metal coordination : bond 0.01650 / 1.02 ( 8) metal coordination : angle 10.34904 / 5.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 MET cc_start: 0.7457 (tpp) cc_final: 0.7145 (tpp) REVERT: D 100 ASP cc_start: 0.6975 (p0) cc_final: 0.6689 (p0) REVERT: D 127 TYR cc_start: 0.7579 (t80) cc_final: 0.7363 (t80) REVERT: B 45 GLN cc_start: 0.9089 (mt0) cc_final: 0.8877 (mt0) REVERT: H 202 GLU cc_start: 0.8358 (mp0) cc_final: 0.7869 (mt-10) REVERT: H 673 LEU cc_start: 0.8611 (tt) cc_final: 0.8311 (tp) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 0.0910 time to fit residues: 20.2486 Evaluate side-chains 162 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 426 ASN Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 665 LEU Chi-restraints excluded: chain H residue 691 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN B 37 GLN ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088501 restraints weight = 18567.598| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.74 r_work: 0.2949 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9981 Z= 0.135 Angle : 0.630 19.053 13886 Z= 0.319 Chirality : 0.043 0.329 1555 Planarity : 0.004 0.059 1528 Dihedral : 23.347 175.980 1931 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.46 % Allowed : 12.44 % Favored : 85.09 % 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 are not related in a simple way. whole: 1.25 (0.27), residues: 1013 helix: 1.59 (0.30), residues: 312 sheet: 1.03 (0.34), residues: 262 loop : 0.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 683 TYR 0.011 0.001 TYR H 117 PHE 0.017 0.001 PHE D 135 TRP 0.015 0.001 TRP D 128 HIS 0.006 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9973) covalent geometry : angle 0.57965 / 0.32 (13874) hydrogen bonds : bond 0.03841 / 2.59 ( 332) hydrogen bonds : angle 3.91912 / 2.76 ( 853) metal coordination : bond 0.00766 / 0.46 ( 8) metal coordination : angle 8.41955 / 4.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 MET cc_start: 0.7602 (tpp) cc_final: 0.7276 (tpp) REVERT: B 45 GLN cc_start: 0.9039 (mt0) cc_final: 0.8816 (mt0) REVERT: H 683 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8565 (ttm170) outliers start: 21 outliers final: 17 residues processed: 163 average time/residue: 0.0943 time to fit residues: 21.1140 Evaluate side-chains 155 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088985 restraints weight = 18572.797| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.76 r_work: 0.2956 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9981 Z= 0.133 Angle : 0.634 17.131 13886 Z= 0.320 Chirality : 0.043 0.321 1555 Planarity : 0.004 0.056 1528 Dihedral : 23.359 178.018 1931 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.46 % Allowed : 13.26 % Favored : 84.27 % 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 are not related in a simple way. whole: 1.40 (0.27), residues: 1013 helix: 1.69 (0.30), residues: 307 sheet: 1.07 (0.34), residues: 262 loop : 0.42 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 427 TYR 0.008 0.001 TYR H 87 PHE 0.013 0.001 PHE D 135 TRP 0.011 0.001 TRP D 128 HIS 0.005 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9973) covalent geometry : angle 0.59197 / 0.32 (13874) hydrogen bonds : bond 0.03692 / 2.47 ( 332) hydrogen bonds : angle 3.86736 / 2.72 ( 853) metal coordination : bond 0.00762 / 0.47 ( 8) metal coordination : angle 7.76579 / 4.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: D 91 MET cc_start: 0.7571 (tpp) cc_final: 0.7160 (tpp) REVERT: D 98 ASP cc_start: 0.8083 (t0) cc_final: 0.7784 (t0) REVERT: D 100 ASP cc_start: 0.6557 (p0) cc_final: 0.6304 (p0) REVERT: B 45 GLN cc_start: 0.9051 (mt0) cc_final: 0.8826 (mt0) REVERT: H 683 ARG cc_start: 0.8838 (tpp80) cc_final: 0.8544 (ttm170) outliers start: 21 outliers final: 19 residues processed: 153 average time/residue: 0.0962 time to fit residues: 19.8200 Evaluate side-chains 153 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 426 ASN Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 691 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.127258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088768 restraints weight = 18509.945| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.74 r_work: 0.2958 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9981 Z= 0.138 Angle : 0.629 16.260 13886 Z= 0.316 Chirality : 0.043 0.313 1555 Planarity : 0.004 0.055 1528 Dihedral : 23.421 178.882 1931 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.58 % Allowed : 13.15 % Favored : 84.27 % 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 are not related in a simple way. whole: 1.38 (0.27), residues: 1013 helix: 1.67 (0.30), residues: 313 sheet: 1.04 (0.34), residues: 264 loop : 0.40 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 4 TYR 0.030 0.001 TYR H 117 PHE 0.014 0.001 PHE D 135 TRP 0.016 0.001 TRP H 671 HIS 0.006 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 9973) covalent geometry : angle 0.58901 / 0.31 (13874) hydrogen bonds : bond 0.03644 / 2.43 ( 332) hydrogen bonds : angle 3.79907 / 2.68 ( 853) metal coordination : bond 0.00769 / 0.48 ( 8) metal coordination : angle 7.53142 / 4.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 MET cc_start: 0.7556 (tpp) cc_final: 0.7119 (tpp) REVERT: D 98 ASP cc_start: 0.8144 (t0) cc_final: 0.7858 (t0) REVERT: D 100 ASP cc_start: 0.6678 (p0) cc_final: 0.6417 (p0) REVERT: B 37 GLN cc_start: 0.8318 (mm110) cc_final: 0.8101 (mm-40) REVERT: B 45 GLN cc_start: 0.9065 (mt0) cc_final: 0.8839 (mt0) REVERT: H 683 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8550 (ttm170) outliers start: 22 outliers final: 19 residues processed: 157 average time/residue: 0.0997 time to fit residues: 20.9568 Evaluate side-chains 156 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 691 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087995 restraints weight = 18510.978| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.65 r_work: 0.2950 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9981 Z= 0.163 Angle : 0.659 16.820 13886 Z= 0.332 Chirality : 0.043 0.312 1555 Planarity : 0.004 0.056 1528 Dihedral : 23.506 178.508 1931 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.58 % Allowed : 13.73 % Favored : 83.69 % 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 are not related in a simple way. whole: 1.27 (0.27), residues: 1013 helix: 1.58 (0.30), residues: 313 sheet: 0.98 (0.34), residues: 264 loop : 0.33 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 427 TYR 0.027 0.001 TYR H 117 PHE 0.018 0.001 PHE D 135 TRP 0.022 0.001 TRP D 128 HIS 0.007 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 9973) covalent geometry : angle 0.61740 / 0.33 (13874) hydrogen bonds : bond 0.03944 / 2.62 ( 332) hydrogen bonds : angle 3.85840 / 2.70 ( 853) metal coordination : bond 0.00845 / 0.53 ( 8) metal coordination : angle 7.87037 / 4.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 91 MET cc_start: 0.7589 (tpp) cc_final: 0.7162 (tpp) REVERT: D 98 ASP cc_start: 0.8183 (t0) cc_final: 0.7900 (t0) REVERT: D 100 ASP cc_start: 0.7020 (p0) cc_final: 0.6757 (p0) REVERT: B 45 GLN cc_start: 0.9067 (mt0) cc_final: 0.8845 (mt0) REVERT: H 683 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8572 (ttm170) outliers start: 22 outliers final: 19 residues processed: 154 average time/residue: 0.0990 time to fit residues: 20.2850 Evaluate side-chains 156 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 691 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 20.0000 chunk 19 optimal weight: 0.0270 chunk 103 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089571 restraints weight = 18250.942| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.51 r_work: 0.2981 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9981 Z= 0.126 Angle : 0.631 15.935 13886 Z= 0.316 Chirality : 0.042 0.308 1555 Planarity : 0.004 0.054 1528 Dihedral : 23.540 178.141 1931 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.46 % Allowed : 13.73 % Favored : 83.80 % 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 are not related in a simple way. whole: 1.32 (0.27), residues: 1013 helix: 1.62 (0.30), residues: 313 sheet: 1.07 (0.35), residues: 261 loop : 0.33 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 517 TYR 0.029 0.001 TYR H 117 PHE 0.016 0.001 PHE D 135 TRP 0.027 0.001 TRP H 671 HIS 0.005 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 9973) covalent geometry : angle 0.59311 / 0.31 (13874) hydrogen bonds : bond 0.03574 / 2.34 ( 332) hydrogen bonds : angle 3.77897 / 2.66 ( 853) metal coordination : bond 0.00698 / 0.42 ( 8) metal coordination : angle 7.37329 / 4.10 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 MET cc_start: 0.7597 (tpp) cc_final: 0.7170 (tpp) REVERT: D 98 ASP cc_start: 0.8166 (t0) cc_final: 0.7888 (t0) REVERT: D 100 ASP cc_start: 0.6994 (p0) cc_final: 0.6741 (p0) REVERT: B 45 GLN cc_start: 0.9025 (mt0) cc_final: 0.8806 (mt0) REVERT: H 427 ARG cc_start: 0.8893 (tpp-160) cc_final: 0.8151 (mmt180) outliers start: 21 outliers final: 19 residues processed: 153 average time/residue: 0.1017 time to fit residues: 20.7667 Evaluate side-chains 155 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 485 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 691 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN H 140 GLN ** H 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.125125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087441 restraints weight = 18339.238| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.50 r_work: 0.2947 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9981 Z= 0.178 Angle : 0.682 18.432 13886 Z= 0.339 Chirality : 0.044 0.309 1555 Planarity : 0.005 0.058 1528 Dihedral : 23.681 178.524 1931 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.11 % Allowed : 14.08 % Favored : 83.80 % 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 are not related in a simple way. whole: 1.20 (0.27), residues: 1013 helix: 1.54 (0.30), residues: 313 sheet: 0.96 (0.35), residues: 257 loop : 0.27 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 427 TYR 0.027 0.002 TYR H 117 PHE 0.013 0.001 PHE D 135 TRP 0.020 0.001 TRP D 128 HIS 0.009 0.001 HIS H 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 9973) covalent geometry : angle 0.63546 / 0.34 (13874) hydrogen bonds : bond 0.04239 / 2.84 ( 332) hydrogen bonds : angle 3.86956 / 2.72 ( 853) metal coordination : bond 0.00904 / 0.57 ( 8) metal coordination : angle 8.48963 / 4.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2081.22 seconds wall clock time: 36 minutes 6.56 seconds (2166.56 seconds total)