Starting phenix.real_space_refine on Sat Sep 12 07:54:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.cif Found real_map, /net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.cif" model { file = "/net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7joa_22409/09_2026/7joa_22409.map" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 25 5.16 5 C 8556 2.51 5 N 2771 2.21 5 O 3351 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14994 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2960 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13969 SG CYS K 384 23.933 65.763 50.961 1.00 90.89 S ATOM 13975 SG CYS K 385 24.055 69.257 48.730 1.00 83.30 S ATOM 14020 SG CYS K 392 23.001 70.170 51.751 1.00 87.81 S Time building chain proxies: 2.99, per 1000 atoms: 0.20 Number of scatterers: 14994 At special positions: 0 Unit cell: (150.15, 110.11, 116.48, 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 1 29.99 S 25 16.00 P 290 15.00 O 3351 8.00 N 2771 7.00 C 8556 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: 1.19 Conformation dependent library (CDL) restraints added in 598.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 385 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " Number of angles added : 3 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.2% alpha, 7.4% beta 138 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.659A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.526A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.609A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.774A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.119A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.529A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.616A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.643A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.898A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.587A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.105A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.949A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.702A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.779A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.188A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.587A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.617A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.642A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.898A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.585A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.104A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 185 removed outlier: 3.797A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA K 167 " --> pdb=" O ASP K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 250 No H-bonds generated for 'chain 'K' and resid 248 through 250' Processing helix chain 'K' and resid 258 through 276 removed outlier: 3.705A pdb=" N GLU K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 removed outlier: 4.399A pdb=" N GLU K 324 " --> pdb=" O SER K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 removed outlier: 4.377A pdb=" N VAL K 336 " --> pdb=" O LEU K 332 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG K 337 " --> pdb=" O GLY K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 Processing helix chain 'K' and resid 393 through 412 Processing helix chain 'K' and resid 413 through 416 Processing helix chain 'K' and resid 419 through 434 removed outlier: 3.847A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 4.038A pdb=" N ASP K 441 " --> pdb=" O SER K 438 " (cutoff:3.500A) Proline residue: K 442 - end of helix Processing helix chain 'K' and resid 444 through 463 removed outlier: 3.525A pdb=" N PHE K 455 " --> pdb=" O LYS K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 500 through 505 removed outlier: 5.995A pdb=" N ILE K 503 " --> pdb=" O GLY K 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.193A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.598A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 8.193A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.953A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.526A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.500A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 8.045A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.626A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP K 281 " --> pdb=" O ARG K 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.626A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'K' and resid 252 through 253 507 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2781 1.33 - 1.45: 4959 1.45 - 1.57: 7503 1.57 - 1.69: 578 1.69 - 1.81: 40 Bond restraints: 15861 Sorted by residual: bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.73e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" N7 DA J 39 " pdb=" C5 DA J 39 " ideal model delta sigma weight residual 1.388 1.366 0.022 6.00e-03 2.78e+04 1.33e+01 bond pdb=" C3' DA I -14 " pdb=" O3' DA I -14 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" C3' DC I -25 " pdb=" C2' DC I -25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20687 1.61 - 3.21: 1810 3.21 - 4.82: 111 4.82 - 6.43: 21 6.43 - 8.03: 5 Bond angle restraints: 22634 Sorted by residual: angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" O4' DA I 43 " pdb=" C4' DA I 43 " pdb=" C3' DA I 43 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.11e+01 angle pdb=" O4' DA J 32 " pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 22629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 7315 33.59 - 67.18: 1493 67.18 - 100.77: 34 100.77 - 134.35: 0 134.35 - 167.94: 1 Dihedral angle restraints: 8843 sinusoidal: 5568 harmonic: 3275 Sorted by residual: dihedral pdb=" CA ASN K 377 " pdb=" C ASN K 377 " pdb=" N HIS K 378 " pdb=" CA HIS K 378 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS D 49 " pdb=" C HIS D 49 " pdb=" N PRO D 50 " pdb=" CA PRO D 50 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA HIS H 49 " pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2177 0.073 - 0.146: 360 0.146 - 0.219: 9 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE K 427 " pdb=" CA ILE K 427 " pdb=" CG1 ILE K 427 " pdb=" CG2 ILE K 427 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE K 269 " pdb=" CA ILE K 269 " pdb=" CG1 ILE K 269 " pdb=" CG2 ILE K 269 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA PHE E 104 " pdb=" N PHE E 104 " pdb=" C PHE E 104 " pdb=" CB PHE E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2544 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 431 " 0.041 2.00e-02 2.50e+03 4.25e-02 4.52e+01 pdb=" CG TRP K 431 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP K 431 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP K 431 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 431 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP K 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 431 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 431 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP K 431 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 454 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ALA K 454 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA K 454 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE K 455 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 446 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C SER K 446 " -0.052 2.00e-02 2.50e+03 pdb=" O SER K 446 " 0.020 2.00e-02 2.50e+03 pdb=" N SER K 447 " 0.018 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1970 2.74 - 3.28: 13642 3.28 - 3.82: 26254 3.82 - 4.36: 30171 4.36 - 4.90: 45898 Nonbonded interactions: 117935 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.206 3.120 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU K 494 " pdb=" ND2 ASN K 498 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG K 394 " pdb=" OD1 ASP K 437 " model vdw 2.249 3.120 nonbonded pdb=" O ILE C 78 " pdb=" OG SER D 55 " model vdw 2.252 3.040 ... (remaining 117930 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.550 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.010 0.515 15865 Z= 0.713 Angle : 0.917 19.373 22637 Z= 0.726 Chirality : 0.051 0.365 2547 Planarity : 0.006 0.054 1861 Dihedral : 25.945 167.942 6725 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.33 (0.24), residues: 1107 helix: 0.88 (0.20), residues: 655 sheet: -0.47 (0.64), residues: 57 loop : -2.08 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 443 TYR 0.017 0.002 TYR K 468 PHE 0.029 0.003 PHE E 104 TRP 0.111 0.008 TRP K 431 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.70 (15861) covalent geometry : angle 0.90253 / 0.72 (22634) hydrogen bonds : bond 0.11476 / 7.44 ( 860) hydrogen bonds : angle 4.73770 / 3.30 ( 2182) metal coordination : bond 0.28123 / 13.63 ( 4) metal coordination : angle 13.94427 / 7.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8066 (m-30) cc_final: 0.7866 (m-30) REVERT: G 74 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7245 (mmmt) REVERT: G 110 ASN cc_start: 0.8076 (t0) cc_final: 0.7852 (t0) REVERT: H 88 THR cc_start: 0.8962 (t) cc_final: 0.8630 (m) REVERT: H 90 THR cc_start: 0.8640 (m) cc_final: 0.8432 (p) REVERT: K 273 GLU cc_start: 0.3902 (mm-30) cc_final: 0.3203 (mm-30) REVERT: K 428 PHE cc_start: 0.6931 (m-10) cc_final: 0.6670 (m-10) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2042 time to fit residues: 63.5997 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 38 ASN D 63 ASN F 25 ASN G 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107090 restraints weight = 24007.963| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.39 r_work: 0.2972 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15865 Z= 0.187 Angle : 0.690 9.976 22637 Z= 0.394 Chirality : 0.049 0.251 2547 Planarity : 0.005 0.046 1861 Dihedral : 29.226 170.472 4411 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.65 % Allowed : 6.81 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.06 (0.25), residues: 1107 helix: 2.06 (0.20), residues: 658 sheet: 0.12 (0.68), residues: 59 loop : -1.68 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.015 0.002 TYR K 346 PHE 0.025 0.002 PHE K 488 TRP 0.048 0.004 TRP K 431 HIS 0.005 0.001 HIS K 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.19 (15861) covalent geometry : angle 0.68953 / 0.39 (22634) hydrogen bonds : bond 0.06903 / 4.72 ( 860) hydrogen bonds : angle 3.06947 / 2.11 ( 2182) metal coordination : bond 0.01665 / 0.86 ( 4) metal coordination : angle 2.69965 / 1.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.310 Fit side-chains REVERT: C 61 GLU cc_start: 0.8246 (tp30) cc_final: 0.7992 (mm-30) REVERT: C 95 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8579 (tttm) REVERT: G 74 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7323 (mmmt) REVERT: G 95 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8624 (tttm) REVERT: K 183 GLN cc_start: 0.6056 (mt0) cc_final: 0.5723 (tm-30) REVERT: K 194 GLN cc_start: 0.5607 (tt0) cc_final: 0.4987 (pp30) REVERT: K 215 MET cc_start: 0.6901 (mmt) cc_final: 0.6624 (mmt) REVERT: K 273 GLU cc_start: 0.3633 (mm-30) cc_final: 0.3122 (mm-30) REVERT: K 496 GLU cc_start: 0.3161 (mm-30) cc_final: 0.2344 (mm-30) outliers start: 16 outliers final: 11 residues processed: 157 average time/residue: 0.1648 time to fit residues: 35.2033 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS D 63 ASN F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108137 restraints weight = 24273.361| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.48 r_work: 0.2959 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15865 Z= 0.142 Angle : 0.606 6.371 22637 Z= 0.350 Chirality : 0.045 0.252 2547 Planarity : 0.004 0.055 1861 Dihedral : 29.195 172.140 4411 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.86 % Allowed : 8.77 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.64 (0.26), residues: 1107 helix: 2.58 (0.20), residues: 660 sheet: 0.45 (0.75), residues: 52 loop : -1.54 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 364 TYR 0.011 0.001 TYR K 346 PHE 0.045 0.002 PHE K 488 TRP 0.025 0.002 TRP K 431 HIS 0.003 0.001 HIS K 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (15861) covalent geometry : angle 0.60534 / 0.35 (22634) hydrogen bonds : bond 0.05778 / 3.96 ( 860) hydrogen bonds : angle 2.82798 / 1.95 ( 2182) metal coordination : bond 0.01493 / 0.78 ( 4) metal coordination : angle 2.66729 / 1.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.444 Fit side-chains REVERT: C 61 GLU cc_start: 0.8333 (tp30) cc_final: 0.8064 (mm-30) REVERT: C 95 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8600 (tttm) REVERT: D 68 ASP cc_start: 0.8640 (t0) cc_final: 0.8437 (t0) REVERT: G 74 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7392 (mmmt) REVERT: G 95 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8569 (tttm) REVERT: K 194 GLN cc_start: 0.5670 (tt0) cc_final: 0.5077 (pp30) REVERT: K 215 MET cc_start: 0.6907 (mmt) cc_final: 0.6542 (mmt) REVERT: K 273 GLU cc_start: 0.3727 (mm-30) cc_final: 0.3128 (mm-30) REVERT: K 313 GLU cc_start: 0.6454 (tm-30) cc_final: 0.5990 (tm-30) REVERT: K 322 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7546 (p) REVERT: K 396 GLU cc_start: 0.6629 (mp0) cc_final: 0.6169 (mp0) outliers start: 18 outliers final: 13 residues processed: 152 average time/residue: 0.1690 time to fit residues: 35.0155 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 0.0870 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109384 restraints weight = 24216.543| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.39 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15865 Z= 0.131 Angle : 0.584 14.462 22637 Z= 0.337 Chirality : 0.043 0.251 2547 Planarity : 0.004 0.039 1861 Dihedral : 29.113 172.090 4411 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.86 % Allowed : 9.49 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.83 (0.25), residues: 1107 helix: 2.71 (0.20), residues: 661 sheet: 0.59 (0.75), residues: 52 loop : -1.47 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 364 TYR 0.009 0.001 TYR K 468 PHE 0.020 0.002 PHE K 488 TRP 0.020 0.002 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 (15861) covalent geometry : angle 0.58381 / 0.34 (22634) hydrogen bonds : bond 0.05174 / 3.55 ( 860) hydrogen bonds : angle 2.70581 / 1.86 ( 2182) metal coordination : bond 0.00462 / 0.24 ( 4) metal coordination : angle 1.82239 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.437 Fit side-chains REVERT: C 95 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8637 (tttm) REVERT: D 63 ASN cc_start: 0.8475 (t0) cc_final: 0.8127 (m-40) REVERT: D 68 ASP cc_start: 0.8597 (t0) cc_final: 0.8346 (t0) REVERT: G 74 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7331 (mmmt) REVERT: G 95 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8592 (tttm) REVERT: K 194 GLN cc_start: 0.5788 (tt0) cc_final: 0.5481 (tm-30) REVERT: K 215 MET cc_start: 0.6935 (mmt) cc_final: 0.6705 (mmt) REVERT: K 273 GLU cc_start: 0.3786 (mm-30) cc_final: 0.3094 (mm-30) REVERT: K 326 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6861 (tt) REVERT: K 329 GLN cc_start: 0.7376 (mp10) cc_final: 0.6676 (pm20) REVERT: K 482 ASP cc_start: 0.3248 (t0) cc_final: 0.2542 (m-30) REVERT: K 496 GLU cc_start: 0.3393 (mm-30) cc_final: 0.2517 (mm-30) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.1669 time to fit residues: 33.0937 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 49 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 24 GLN D 47 GLN E 68 GLN G 24 GLN H 47 GLN K 429 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.146848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107857 restraints weight = 24089.330| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.35 r_work: 0.2987 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15865 Z= 0.138 Angle : 0.579 10.346 22637 Z= 0.332 Chirality : 0.043 0.248 2547 Planarity : 0.004 0.039 1861 Dihedral : 29.158 173.037 4411 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 10.42 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.96 (0.25), residues: 1107 helix: 2.84 (0.20), residues: 656 sheet: 0.60 (0.74), residues: 52 loop : -1.40 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.007 0.001 TYR F 51 PHE 0.020 0.002 PHE K 488 TRP 0.032 0.003 TRP K 431 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (15861) covalent geometry : angle 0.57856 / 0.33 (22634) hydrogen bonds : bond 0.05377 / 3.69 ( 860) hydrogen bonds : angle 2.66559 / 1.85 ( 2182) metal coordination : bond 0.01103 / 0.58 ( 4) metal coordination : angle 1.26470 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.450 Fit side-chains REVERT: C 95 LYS cc_start: 0.9124 (ttmm) cc_final: 0.8631 (tttm) REVERT: D 63 ASN cc_start: 0.8418 (t0) cc_final: 0.8061 (m-40) REVERT: G 74 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7299 (mmmt) REVERT: G 95 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8561 (tttm) REVERT: K 194 GLN cc_start: 0.5947 (tt0) cc_final: 0.5663 (tm-30) REVERT: K 215 MET cc_start: 0.6885 (mmt) cc_final: 0.6677 (mmt) REVERT: K 273 GLU cc_start: 0.3781 (mm-30) cc_final: 0.3092 (mm-30) REVERT: K 322 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7611 (p) REVERT: K 326 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6745 (tt) REVERT: K 482 ASP cc_start: 0.3313 (t0) cc_final: 0.2599 (m-30) REVERT: K 496 GLU cc_start: 0.3378 (mm-30) cc_final: 0.2536 (mm-30) REVERT: K 501 PHE cc_start: 0.4733 (m-80) cc_final: 0.4428 (m-80) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.1683 time to fit residues: 32.4425 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 0.0970 chunk 74 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 47 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.146515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106864 restraints weight = 24073.298| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.22 r_work: 0.2991 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15865 Z= 0.139 Angle : 0.576 7.780 22637 Z= 0.330 Chirality : 0.043 0.247 2547 Planarity : 0.004 0.036 1861 Dihedral : 29.176 173.796 4411 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 10.94 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 2.01 (0.25), residues: 1107 helix: 2.83 (0.20), residues: 657 sheet: 0.77 (0.73), residues: 52 loop : -1.29 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 364 TYR 0.008 0.001 TYR F 51 PHE 0.026 0.002 PHE K 501 TRP 0.016 0.002 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (15861) covalent geometry : angle 0.57550 / 0.33 (22634) hydrogen bonds : bond 0.05440 / 3.74 ( 860) hydrogen bonds : angle 2.62375 / 1.84 ( 2182) metal coordination : bond 0.00853 / 0.44 ( 4) metal coordination : angle 2.17206 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.447 Fit side-chains REVERT: C 95 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8608 (tttm) REVERT: G 74 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7494 (mmmt) REVERT: G 95 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8532 (tttm) REVERT: H 68 ASP cc_start: 0.8540 (t0) cc_final: 0.8284 (t0) REVERT: K 194 GLN cc_start: 0.6048 (tt0) cc_final: 0.5743 (tm-30) REVERT: K 215 MET cc_start: 0.6973 (mmt) cc_final: 0.6754 (mmt) REVERT: K 273 GLU cc_start: 0.3786 (mm-30) cc_final: 0.3065 (mm-30) REVERT: K 322 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7661 (p) REVERT: K 396 GLU cc_start: 0.6487 (mp0) cc_final: 0.6027 (mp0) REVERT: K 482 ASP cc_start: 0.3311 (t0) cc_final: 0.2610 (m-30) REVERT: K 496 GLU cc_start: 0.3634 (mm-30) cc_final: 0.2843 (mm-30) REVERT: K 501 PHE cc_start: 0.3642 (m-80) cc_final: 0.3373 (m-80) outliers start: 16 outliers final: 11 residues processed: 142 average time/residue: 0.1705 time to fit residues: 33.1607 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 94 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107758 restraints weight = 23892.779| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.34 r_work: 0.2995 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15865 Z= 0.128 Angle : 0.560 9.536 22637 Z= 0.323 Chirality : 0.042 0.251 2547 Planarity : 0.004 0.036 1861 Dihedral : 29.148 173.786 4411 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.75 % Allowed : 11.56 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 2.11 (0.25), residues: 1107 helix: 2.89 (0.20), residues: 658 sheet: 0.80 (0.74), residues: 52 loop : -1.23 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.007 0.001 TYR F 51 PHE 0.018 0.001 PHE K 488 TRP 0.019 0.002 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (15861) covalent geometry : angle 0.55938 / 0.32 (22634) hydrogen bonds : bond 0.05095 / 3.51 ( 860) hydrogen bonds : angle 2.58482 / 1.80 ( 2182) metal coordination : bond 0.00609 / 0.32 ( 4) metal coordination : angle 1.68195 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.443 Fit side-chains REVERT: C 95 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8646 (tttm) REVERT: D 33 ARG cc_start: 0.7452 (ptt180) cc_final: 0.7223 (ptt180) REVERT: D 63 ASN cc_start: 0.8357 (t0) cc_final: 0.8069 (m-40) REVERT: G 74 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7368 (mmmt) REVERT: G 95 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8534 (tttm) REVERT: H 68 ASP cc_start: 0.8524 (t0) cc_final: 0.8233 (t0) REVERT: K 194 GLN cc_start: 0.6075 (tt0) cc_final: 0.5788 (tm-30) REVERT: K 273 GLU cc_start: 0.3958 (mm-30) cc_final: 0.3307 (mm-30) REVERT: K 322 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7662 (p) REVERT: K 396 GLU cc_start: 0.6430 (mp0) cc_final: 0.5945 (mp0) REVERT: K 482 ASP cc_start: 0.3306 (t0) cc_final: 0.2602 (m-30) REVERT: K 496 GLU cc_start: 0.3647 (mm-30) cc_final: 0.2759 (mm-30) REVERT: K 501 PHE cc_start: 0.3680 (m-80) cc_final: 0.3461 (m-10) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1659 time to fit residues: 30.3300 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109416 restraints weight = 24066.686| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.51 r_work: 0.2992 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15865 Z= 0.129 Angle : 0.553 8.718 22637 Z= 0.320 Chirality : 0.042 0.249 2547 Planarity : 0.004 0.034 1861 Dihedral : 29.129 174.435 4411 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 12.07 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 2.21 (0.25), residues: 1107 helix: 2.95 (0.20), residues: 661 sheet: 0.90 (0.72), residues: 52 loop : -1.18 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 364 TYR 0.008 0.001 TYR G 57 PHE 0.021 0.002 PHE K 488 TRP 0.025 0.003 TRP K 431 HIS 0.005 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (15861) covalent geometry : angle 0.55292 / 0.32 (22634) hydrogen bonds : bond 0.05091 / 3.50 ( 860) hydrogen bonds : angle 2.54967 / 1.78 ( 2182) metal coordination : bond 0.00634 / 0.33 ( 4) metal coordination : angle 1.46704 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.424 Fit side-chains REVERT: C 95 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8659 (tttm) REVERT: D 33 ARG cc_start: 0.7523 (ptt180) cc_final: 0.7284 (ptt180) REVERT: D 63 ASN cc_start: 0.8348 (t0) cc_final: 0.8078 (m-40) REVERT: G 74 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7403 (mmmt) REVERT: G 95 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8514 (tttm) REVERT: K 194 GLN cc_start: 0.6056 (tt0) cc_final: 0.5801 (tm-30) REVERT: K 273 GLU cc_start: 0.3669 (mm-30) cc_final: 0.2697 (mt-10) REVERT: K 313 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6462 (tm-30) REVERT: K 322 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7587 (p) REVERT: K 396 GLU cc_start: 0.6494 (mp0) cc_final: 0.6026 (mp0) REVERT: K 482 ASP cc_start: 0.3376 (t0) cc_final: 0.2673 (m-30) REVERT: K 496 GLU cc_start: 0.3451 (mm-30) cc_final: 0.2585 (mm-30) outliers start: 16 outliers final: 15 residues processed: 137 average time/residue: 0.1656 time to fit residues: 31.0997 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107829 restraints weight = 23954.308| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.22 r_work: 0.3012 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15865 Z= 0.135 Angle : 0.566 8.563 22637 Z= 0.324 Chirality : 0.043 0.247 2547 Planarity : 0.004 0.038 1861 Dihedral : 29.111 175.047 4411 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.55 % Allowed : 12.07 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 2.22 (0.25), residues: 1107 helix: 2.91 (0.20), residues: 666 sheet: 0.95 (0.71), residues: 52 loop : -1.17 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 364 TYR 0.010 0.001 TYR K 346 PHE 0.041 0.002 PHE K 488 TRP 0.029 0.003 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (15861) covalent geometry : angle 0.56614 / 0.32 (22634) hydrogen bonds : bond 0.05367 / 3.69 ( 860) hydrogen bonds : angle 2.58864 / 1.81 ( 2182) metal coordination : bond 0.00623 / 0.32 ( 4) metal coordination : angle 1.58954 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.458 Fit side-chains REVERT: C 95 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8658 (tttm) REVERT: D 33 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7308 (ptt180) REVERT: G 74 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7522 (mmmt) REVERT: G 95 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8545 (tttm) REVERT: H 68 ASP cc_start: 0.8498 (t0) cc_final: 0.8296 (t0) REVERT: K 273 GLU cc_start: 0.3596 (mm-30) cc_final: 0.3017 (mm-30) REVERT: K 313 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6457 (tm-30) REVERT: K 322 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7703 (p) REVERT: K 396 GLU cc_start: 0.6568 (mp0) cc_final: 0.6098 (mp0) REVERT: K 482 ASP cc_start: 0.3396 (t0) cc_final: 0.2772 (m-30) REVERT: K 496 GLU cc_start: 0.3545 (mm-30) cc_final: 0.2826 (mm-30) outliers start: 15 outliers final: 13 residues processed: 134 average time/residue: 0.1612 time to fit residues: 30.1493 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 499 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.0970 chunk 100 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN E 76 GLN K 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107210 restraints weight = 23878.063| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.23 r_work: 0.3000 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15865 Z= 0.127 Angle : 0.566 16.751 22637 Z= 0.322 Chirality : 0.042 0.251 2547 Planarity : 0.004 0.033 1861 Dihedral : 29.074 174.849 4411 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.55 % Allowed : 12.59 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 2.24 (0.25), residues: 1107 helix: 2.92 (0.20), residues: 666 sheet: 0.96 (0.70), residues: 52 loop : -1.14 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 364 TYR 0.008 0.001 TYR K 346 PHE 0.042 0.002 PHE K 488 TRP 0.036 0.003 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (15861) covalent geometry : angle 0.56553 / 0.32 (22634) hydrogen bonds : bond 0.05093 / 3.50 ( 860) hydrogen bonds : angle 2.57096 / 1.79 ( 2182) metal coordination : bond 0.00554 / 0.29 ( 4) metal coordination : angle 1.45770 / 0.77 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.357 Fit side-chains REVERT: C 95 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8661 (tttm) REVERT: D 33 ARG cc_start: 0.7596 (ptt180) cc_final: 0.7373 (ptt180) REVERT: G 42 ARG cc_start: 0.9080 (ptm-80) cc_final: 0.8725 (mtm110) REVERT: G 74 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7511 (mmmt) REVERT: G 95 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8539 (tttm) REVERT: H 68 ASP cc_start: 0.8507 (t0) cc_final: 0.8301 (t0) REVERT: K 273 GLU cc_start: 0.3578 (mm-30) cc_final: 0.2990 (mm-30) REVERT: K 313 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6447 (tm-30) REVERT: K 322 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7686 (p) REVERT: K 396 GLU cc_start: 0.6610 (mp0) cc_final: 0.6144 (mp0) REVERT: K 431 TRP cc_start: 0.6893 (m-10) cc_final: 0.6645 (m-10) REVERT: K 482 ASP cc_start: 0.3398 (t0) cc_final: 0.2771 (m-30) outliers start: 15 outliers final: 14 residues processed: 131 average time/residue: 0.1550 time to fit residues: 28.2691 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 499 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 83 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.0370 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108211 restraints weight = 23876.215| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.25 r_work: 0.3014 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 15865 Z= 0.156 Angle : 0.763 59.196 22637 Z= 0.456 Chirality : 0.042 0.251 2547 Planarity : 0.004 0.049 1861 Dihedral : 29.075 174.853 4411 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 12.80 % Favored : 85.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.63 % 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: 2.24 (0.25), residues: 1107 helix: 2.92 (0.20), residues: 666 sheet: 0.97 (0.70), residues: 52 loop : -1.14 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 364 TYR 0.008 0.001 TYR K 346 PHE 0.038 0.002 PHE K 488 TRP 0.032 0.003 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (15861) covalent geometry : angle 0.76285 / 0.46 (22634) hydrogen bonds : bond 0.05091 / 3.50 ( 860) hydrogen bonds : angle 2.57983 / 1.80 ( 2182) metal coordination : bond 0.00555 / 0.29 ( 4) metal coordination : angle 1.45821 / 0.77 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.53 seconds wall clock time: 56 minutes 0.58 seconds (3360.58 seconds total)