Starting phenix.real_space_refine on Wed Mar 4 15:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7joa_22409/03_2026/7joa_22409.cif Found real_map, /net/cci-nas-00/data/ceres_data/7joa_22409/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7joa_22409/03_2026/7joa_22409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7joa_22409/03_2026/7joa_22409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7joa_22409/03_2026/7joa_22409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7joa_22409/03_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-dev-5986/lib/python3.9/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: 3.25, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 484.5 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: 1.86 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: 3.16 Time building geometry restraints manager: 1.32 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=" CA GLN A 55 " pdb=" C GLN A 55 " ideal model delta sigma weight residual 1.524 1.471 0.052 2.25e-02 1.98e+03 5.37e+00 bond pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 1.523 1.496 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.422 1.381 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CG ARG F 39 " pdb=" CD ARG F 39 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CB VAL F 43 " pdb=" CG2 VAL F 43 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 21417 1.61 - 3.21: 1107 3.21 - 4.82: 84 4.82 - 6.43: 21 6.43 - 8.03: 5 Bond angle restraints: 22634 Sorted by residual: angle pdb=" N TRP K 431 " pdb=" CA TRP K 431 " pdb=" CB TRP K 431 " ideal model delta sigma weight residual 110.28 116.47 -6.19 1.55e+00 4.16e-01 1.60e+01 angle pdb=" C TYR A 54 " pdb=" N GLN A 55 " pdb=" CA GLN A 55 " ideal model delta sigma weight residual 122.55 114.52 8.03 2.03e+00 2.43e-01 1.57e+01 angle pdb=" C PHE E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta sigma weight residual 120.29 115.67 4.62 1.42e+00 4.96e-01 1.06e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.93e+00 angle pdb=" C ARG K 461 " pdb=" N THR K 462 " pdb=" CA THR K 462 " ideal model delta sigma weight residual 122.38 117.80 4.58 1.81e+00 3.05e-01 6.39e+00 ... (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: 2318 0.073 - 0.146: 223 0.146 - 0.219: 5 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: 3.070 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.970 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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= 0.403 Angle : 0.796 19.373 22637 Z= 0.466 Chirality : 0.045 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 covalent geometry : bond 0.00861 (15861) covalent geometry : angle 0.78016 (22634) hydrogen bonds : bond 0.11476 ( 860) hydrogen bonds : angle 4.73770 ( 2182) metal coordination : bond 0.28123 ( 4) metal coordination : angle 13.94427 ( 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 : 0.383 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8066 (m-30) cc_final: 0.7862 (m-30) REVERT: G 74 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7246 (mmmt) REVERT: G 110 ASN cc_start: 0.8076 (t0) cc_final: 0.7854 (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: 0.3206 (mm-30) REVERT: K 428 PHE cc_start: 0.6931 (m-10) cc_final: 0.6671 (m-10) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1995 time to fit residues: 61.4840 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 : 0.435 ------------------------------------------------------------------------------- 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: 4.9990 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: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 25 ASN C 24 GLN C 38 ASN D 47 GLN F 25 ASN F 75 HIS G 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106454 restraints weight = 23740.007| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.35 r_work: 0.2954 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15865 Z= 0.174 Angle : 0.579 7.984 22637 Z= 0.341 Chirality : 0.036 0.139 2547 Planarity : 0.004 0.047 1861 Dihedral : 28.964 171.692 4411 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 6.50 % Favored : 92.05 % 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: 1.30 (0.26), residues: 1107 helix: 2.38 (0.20), residues: 654 sheet: 0.22 (0.72), residues: 52 loop : -1.76 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 180 TYR 0.017 0.002 TYR K 346 PHE 0.019 0.003 PHE K 488 TRP 0.040 0.004 TRP K 431 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00383 (15861) covalent geometry : angle 0.57822 (22634) hydrogen bonds : bond 0.05696 ( 860) hydrogen bonds : angle 2.86406 ( 2182) metal coordination : bond 0.01288 ( 4) metal coordination : angle 1.80223 ( 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: 14 poor density : 150 time to evaluate : 0.429 Fit side-chains REVERT: A 56 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8707 (tttp) REVERT: A 76 GLN cc_start: 0.7683 (tp40) cc_final: 0.7471 (tt0) REVERT: C 61 GLU cc_start: 0.8355 (tp30) cc_final: 0.8054 (mm-30) REVERT: C 95 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8562 (tttm) REVERT: G 74 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7383 (mmmt) REVERT: G 95 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8571 (tttm) REVERT: K 183 GLN cc_start: 0.5924 (mt0) cc_final: 0.5661 (tm-30) REVERT: K 194 GLN cc_start: 0.5644 (tt0) cc_final: 0.5381 (tm-30) REVERT: K 215 MET cc_start: 0.6849 (mmt) cc_final: 0.6570 (mmt) REVERT: K 273 GLU cc_start: 0.3530 (mm-30) cc_final: 0.2956 (mm-30) outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 0.1794 time to fit residues: 37.9188 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 : 0.421 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN D 63 ASN E 68 GLN G 24 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108644 restraints weight = 24234.611| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.43 r_work: 0.2980 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15865 Z= 0.145 Angle : 0.524 10.992 22637 Z= 0.310 Chirality : 0.034 0.123 2547 Planarity : 0.004 0.042 1861 Dihedral : 28.792 172.556 4411 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.34 % Allowed : 8.36 % Favored : 90.30 % 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: 1.74 (0.26), residues: 1107 helix: 2.70 (0.20), residues: 657 sheet: 0.51 (0.73), residues: 52 loop : -1.57 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 483 TYR 0.009 0.001 TYR K 346 PHE 0.013 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 covalent geometry : bond 0.00310 (15861) covalent geometry : angle 0.52388 (22634) hydrogen bonds : bond 0.04662 ( 860) hydrogen bonds : angle 2.60934 ( 2182) metal coordination : bond 0.00944 ( 4) metal coordination : angle 2.04334 ( 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 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.448 Fit side-chains REVERT: C 61 GLU cc_start: 0.8310 (tp30) cc_final: 0.8022 (mm-30) REVERT: C 95 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8573 (tttm) REVERT: D 93 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: F 80 THR cc_start: 0.8924 (m) cc_final: 0.8696 (t) REVERT: G 74 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7397 (mmmt) REVERT: G 95 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8549 (tttm) REVERT: G 99 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8711 (mtmt) REVERT: K 194 GLN cc_start: 0.5947 (tt0) cc_final: 0.5617 (tm-30) REVERT: K 215 MET cc_start: 0.7023 (mmt) cc_final: 0.6767 (mmt) REVERT: K 273 GLU cc_start: 0.3376 (mm-30) cc_final: 0.2691 (mm-30) REVERT: K 396 GLU cc_start: 0.6659 (mp0) cc_final: 0.6228 (mp0) REVERT: K 464 LYS cc_start: 0.4339 (tptp) cc_final: 0.3612 (tttm) REVERT: K 496 GLU cc_start: 0.3469 (mm-30) cc_final: 0.2761 (mm-30) outliers start: 13 outliers final: 12 residues processed: 144 average time/residue: 0.1709 time to fit residues: 33.0304 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 93 GLU 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 K residue 155 ASP Chi-restraints excluded: chain K residue 309 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 129 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.146933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107492 restraints weight = 23994.026| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.28 r_work: 0.2997 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15865 Z= 0.145 Angle : 0.515 8.172 22637 Z= 0.305 Chirality : 0.034 0.124 2547 Planarity : 0.004 0.039 1861 Dihedral : 28.720 173.632 4411 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.65 % Allowed : 9.29 % Favored : 89.06 % 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: 1.86 (0.25), residues: 1107 helix: 2.76 (0.20), residues: 665 sheet: 0.69 (0.73), residues: 52 loop : -1.56 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 364 TYR 0.010 0.001 TYR K 346 PHE 0.022 0.002 PHE K 504 TRP 0.018 0.002 TRP K 431 HIS 0.005 0.001 HIS K 369 Details of bonding type rmsd covalent geometry : bond 0.00310 (15861) covalent geometry : angle 0.51451 (22634) hydrogen bonds : bond 0.04777 ( 860) hydrogen bonds : angle 2.55377 ( 2182) metal coordination : bond 0.00548 ( 4) metal coordination : angle 1.71043 ( 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 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.434 Fit side-chains REVERT: C 42 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8639 (mtm110) REVERT: C 61 GLU cc_start: 0.8268 (tp30) cc_final: 0.7968 (mm-30) REVERT: C 95 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8578 (tttm) REVERT: D 63 ASN cc_start: 0.8327 (t0) cc_final: 0.8027 (m-40) REVERT: G 74 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7418 (mmmt) REVERT: G 95 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8480 (tttm) REVERT: G 99 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8701 (mtmt) REVERT: G 104 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7955 (mm-40) REVERT: H 63 ASN cc_start: 0.8298 (t0) cc_final: 0.8015 (m-40) REVERT: K 194 GLN cc_start: 0.6030 (tt0) cc_final: 0.5816 (tm-30) REVERT: K 215 MET cc_start: 0.6859 (mmt) cc_final: 0.6654 (mmt) REVERT: K 273 GLU cc_start: 0.3319 (mm-30) cc_final: 0.2503 (mm-30) REVERT: K 322 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7559 (p) REVERT: K 396 GLU cc_start: 0.6682 (mp0) cc_final: 0.6264 (mp0) REVERT: K 482 ASP cc_start: 0.3581 (t0) cc_final: 0.2764 (m-30) REVERT: K 491 LYS cc_start: 0.5108 (mttt) cc_final: 0.4701 (ptmt) REVERT: K 496 GLU cc_start: 0.3375 (mm-30) cc_final: 0.2631 (mm-30) REVERT: K 501 PHE cc_start: 0.4240 (m-80) cc_final: 0.4014 (m-80) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.1797 time to fit residues: 33.7385 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 108 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.148658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108629 restraints weight = 24086.056| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.20 r_work: 0.3016 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15865 Z= 0.134 Angle : 0.505 12.266 22637 Z= 0.298 Chirality : 0.033 0.145 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.662 173.583 4411 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.34 % Allowed : 10.53 % Favored : 88.13 % 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: 2.02 (0.25), residues: 1107 helix: 2.83 (0.20), residues: 666 sheet: 0.78 (0.71), residues: 52 loop : -1.39 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 364 TYR 0.009 0.001 TYR K 346 PHE 0.008 0.001 PHE G 25 TRP 0.014 0.002 TRP K 431 HIS 0.004 0.001 HIS K 369 Details of bonding type rmsd covalent geometry : bond 0.00282 (15861) covalent geometry : angle 0.50442 (22634) hydrogen bonds : bond 0.04431 ( 860) hydrogen bonds : angle 2.51184 ( 2182) metal coordination : bond 0.00500 ( 4) metal coordination : angle 1.61268 ( 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 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.333 Fit side-chains REVERT: C 42 ARG cc_start: 0.9021 (ptm-80) cc_final: 0.8683 (mtm110) REVERT: C 61 GLU cc_start: 0.8298 (tp30) cc_final: 0.8003 (mm-30) REVERT: C 95 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8656 (tttm) REVERT: D 33 ARG cc_start: 0.7556 (ptt180) cc_final: 0.7319 (ptt180) REVERT: D 63 ASN cc_start: 0.8296 (t0) cc_final: 0.8037 (m-40) REVERT: D 93 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: G 74 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7427 (mmmt) REVERT: G 95 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8558 (tttm) REVERT: G 104 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7926 (mm-40) REVERT: H 63 ASN cc_start: 0.8256 (t0) cc_final: 0.8013 (m-40) REVERT: K 253 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6525 (pt0) REVERT: K 273 GLU cc_start: 0.3321 (mm-30) cc_final: 0.2848 (mm-30) REVERT: K 322 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7485 (p) REVERT: K 396 GLU cc_start: 0.6708 (mp0) cc_final: 0.6327 (mp0) REVERT: K 482 ASP cc_start: 0.3606 (t0) cc_final: 0.2797 (m-30) REVERT: K 496 GLU cc_start: 0.3383 (mm-30) cc_final: 0.2768 (mm-30) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.1818 time to fit residues: 34.4758 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 93 GLU 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 309 ILE Chi-restraints excluded: chain K residue 322 THR 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: 3.9990 chunk 74 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102290 restraints weight = 23931.705| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.55 r_work: 0.2917 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15865 Z= 0.177 Angle : 0.554 10.972 22637 Z= 0.323 Chirality : 0.035 0.138 2547 Planarity : 0.004 0.036 1861 Dihedral : 28.783 175.547 4411 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.55 % Allowed : 10.63 % Favored : 87.82 % 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: 1.91 (0.25), residues: 1107 helix: 2.75 (0.20), residues: 665 sheet: 0.75 (0.71), residues: 52 loop : -1.45 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 364 TYR 0.017 0.002 TYR K 495 PHE 0.015 0.002 PHE C 25 TRP 0.018 0.002 TRP K 431 HIS 0.004 0.001 HIS K 369 Details of bonding type rmsd covalent geometry : bond 0.00395 (15861) covalent geometry : angle 0.55337 (22634) hydrogen bonds : bond 0.05834 ( 860) hydrogen bonds : angle 2.64261 ( 2182) metal coordination : bond 0.00915 ( 4) metal coordination : angle 1.79547 ( 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 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.452 Fit side-chains REVERT: C 61 GLU cc_start: 0.8423 (tp30) cc_final: 0.8155 (mm-30) REVERT: C 95 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8657 (tttm) REVERT: D 33 ARG cc_start: 0.7556 (ptt180) cc_final: 0.7304 (ptt180) REVERT: D 93 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: E 56 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8858 (tttp) REVERT: G 42 ARG cc_start: 0.9144 (ptm-80) cc_final: 0.8790 (mtm110) REVERT: G 74 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7530 (mmmt) REVERT: G 95 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8528 (tttm) REVERT: K 273 GLU cc_start: 0.3601 (mm-30) cc_final: 0.2710 (mt-10) REVERT: K 322 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7837 (p) REVERT: K 396 GLU cc_start: 0.6545 (mp0) cc_final: 0.6129 (mp0) REVERT: K 482 ASP cc_start: 0.3443 (t0) cc_final: 0.2755 (m-30) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.1763 time to fit residues: 30.9800 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 93 GLU 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 375 LEU 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: 4.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100143 restraints weight = 23505.309| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.52 r_work: 0.2865 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15865 Z= 0.230 Angle : 0.611 9.377 22637 Z= 0.353 Chirality : 0.038 0.134 2547 Planarity : 0.005 0.047 1861 Dihedral : 28.926 177.856 4411 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.24 % Allowed : 11.46 % Favored : 87.31 % 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: 1.59 (0.25), residues: 1107 helix: 2.46 (0.20), residues: 665 sheet: 0.81 (0.67), residues: 52 loop : -1.52 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 364 TYR 0.020 0.002 TYR K 495 PHE 0.018 0.002 PHE C 25 TRP 0.022 0.003 TRP K 431 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00533 (15861) covalent geometry : angle 0.61020 (22634) hydrogen bonds : bond 0.06953 ( 860) hydrogen bonds : angle 2.80560 ( 2182) metal coordination : bond 0.01402 ( 4) metal coordination : angle 2.19862 ( 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 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.319 Fit side-chains REVERT: C 61 GLU cc_start: 0.8478 (tp30) cc_final: 0.8253 (mm-30) REVERT: C 95 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8664 (tttm) REVERT: D 33 ARG cc_start: 0.7687 (ptt180) cc_final: 0.7415 (ptt180) REVERT: D 93 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: E 56 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8885 (tttp) REVERT: G 74 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7571 (mmmt) REVERT: G 95 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8561 (tttm) REVERT: K 194 GLN cc_start: 0.5981 (tt0) cc_final: 0.5678 (tp40) REVERT: K 273 GLU cc_start: 0.3979 (mm-30) cc_final: 0.3094 (mt-10) REVERT: K 396 GLU cc_start: 0.6354 (mp0) cc_final: 0.5863 (mp0) REVERT: K 482 ASP cc_start: 0.3516 (t0) cc_final: 0.2838 (m-30) outliers start: 12 outliers final: 11 residues processed: 134 average time/residue: 0.1575 time to fit residues: 28.5999 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 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 88 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR 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: 0.9990 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102217 restraints weight = 23840.322| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.56 r_work: 0.2910 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15865 Z= 0.147 Angle : 0.554 8.952 22637 Z= 0.328 Chirality : 0.036 0.152 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.822 176.358 4411 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.24 % Allowed : 11.56 % Favored : 87.20 % 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: 1.82 (0.25), residues: 1107 helix: 2.63 (0.20), residues: 665 sheet: 0.88 (0.65), residues: 52 loop : -1.41 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 364 TYR 0.024 0.001 TYR K 495 PHE 0.021 0.001 PHE K 428 TRP 0.032 0.003 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd covalent geometry : bond 0.00306 (15861) covalent geometry : angle 0.55354 (22634) hydrogen bonds : bond 0.05619 ( 860) hydrogen bonds : angle 2.69960 ( 2182) metal coordination : bond 0.00945 ( 4) metal coordination : angle 1.76933 ( 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 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.400 Fit side-chains REVERT: A 42 ARG cc_start: 0.8640 (mtp-110) cc_final: 0.8414 (mtp-110) REVERT: C 61 GLU cc_start: 0.8431 (tp30) cc_final: 0.8198 (mm-30) REVERT: C 95 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8665 (tttm) REVERT: D 33 ARG cc_start: 0.7605 (ptt180) cc_final: 0.7328 (ptt180) REVERT: D 93 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: G 42 ARG cc_start: 0.9066 (ptm-80) cc_final: 0.8688 (mtm110) REVERT: G 74 LYS cc_start: 0.8356 (mtmm) cc_final: 0.7424 (mmmt) REVERT: G 95 LYS cc_start: 0.9095 (ttpt) cc_final: 0.8554 (tttm) REVERT: K 194 GLN cc_start: 0.6000 (tt0) cc_final: 0.5799 (tp40) REVERT: K 273 GLU cc_start: 0.4198 (mm-30) cc_final: 0.3797 (mm-30) REVERT: K 396 GLU cc_start: 0.6428 (mp0) cc_final: 0.5991 (mp0) REVERT: K 482 ASP cc_start: 0.3458 (t0) cc_final: 0.2780 (m-30) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.1714 time to fit residues: 29.4552 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 93 GLU 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 375 LEU 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: 0.7980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100965 restraints weight = 23679.054| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.53 r_work: 0.2888 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15865 Z= 0.175 Angle : 0.558 8.746 22637 Z= 0.328 Chirality : 0.036 0.147 2547 Planarity : 0.004 0.038 1861 Dihedral : 28.791 177.343 4411 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 11.76 % Favored : 87.20 % 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: 1.88 (0.25), residues: 1107 helix: 2.67 (0.20), residues: 665 sheet: 1.09 (0.66), residues: 52 loop : -1.39 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 364 TYR 0.022 0.001 TYR K 495 PHE 0.013 0.002 PHE C 25 TRP 0.039 0.003 TRP K 431 HIS 0.004 0.001 HIS K 369 Details of bonding type rmsd covalent geometry : bond 0.00391 (15861) covalent geometry : angle 0.55722 (22634) hydrogen bonds : bond 0.05724 ( 860) hydrogen bonds : angle 2.64476 ( 2182) metal coordination : bond 0.01076 ( 4) metal coordination : angle 1.73272 ( 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 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.341 Fit side-chains REVERT: C 61 GLU cc_start: 0.8475 (tp30) cc_final: 0.8260 (mm-30) REVERT: C 95 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8676 (tttm) REVERT: D 93 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: E 56 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8869 (tttp) REVERT: G 74 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7506 (mmmt) REVERT: G 95 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8543 (tttm) REVERT: H 33 ARG cc_start: 0.7499 (ptt180) cc_final: 0.7227 (ptt180) REVERT: K 194 GLN cc_start: 0.5936 (tt0) cc_final: 0.5731 (tp40) REVERT: K 273 GLU cc_start: 0.4173 (mm-30) cc_final: 0.3341 (mt-10) REVERT: K 322 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7644 (p) REVERT: K 396 GLU cc_start: 0.6493 (mp0) cc_final: 0.6080 (mp0) REVERT: K 491 LYS cc_start: 0.5194 (mptt) cc_final: 0.4530 (ptmt) outliers start: 10 outliers final: 8 residues processed: 122 average time/residue: 0.1744 time to fit residues: 28.5434 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 93 GLU 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 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099790 restraints weight = 23502.782| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.61 r_work: 0.2846 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15865 Z= 0.238 Angle : 0.616 8.440 22637 Z= 0.357 Chirality : 0.039 0.151 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.907 178.755 4411 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 11.66 % Favored : 87.20 % 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 (0.25), residues: 1107 helix: 2.40 (0.20), residues: 670 sheet: 1.01 (0.65), residues: 52 loop : -1.40 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 364 TYR 0.021 0.002 TYR K 495 PHE 0.019 0.002 PHE C 25 TRP 0.043 0.004 TRP K 431 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00551 (15861) covalent geometry : angle 0.61606 (22634) hydrogen bonds : bond 0.06976 ( 860) hydrogen bonds : angle 2.77418 ( 2182) metal coordination : bond 0.01493 ( 4) metal coordination : angle 1.82232 ( 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 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.438 Fit side-chains REVERT: C 61 GLU cc_start: 0.8508 (tp30) cc_final: 0.8296 (mm-30) REVERT: C 95 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8658 (tttm) REVERT: D 93 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: E 56 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8903 (tttp) REVERT: G 74 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7569 (mmmt) REVERT: G 95 LYS cc_start: 0.9148 (ttpt) cc_final: 0.8553 (tttm) REVERT: H 33 ARG cc_start: 0.7542 (ptt180) cc_final: 0.7274 (ptt180) REVERT: K 194 GLN cc_start: 0.5975 (tt0) cc_final: 0.5739 (tp40) REVERT: K 273 GLU cc_start: 0.4170 (mm-30) cc_final: 0.3131 (mt-10) REVERT: K 322 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7719 (p) REVERT: K 396 GLU cc_start: 0.6267 (mp0) cc_final: 0.5802 (mp0) REVERT: K 431 TRP cc_start: 0.6724 (m-90) cc_final: 0.5921 (m-90) REVERT: K 482 ASP cc_start: 0.3603 (t0) cc_final: 0.2881 (m-30) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.1671 time to fit residues: 28.8722 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 83 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102932 restraints weight = 23532.184| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.53 r_work: 0.2858 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15865 Z= 0.206 Angle : 0.602 14.066 22637 Z= 0.349 Chirality : 0.038 0.142 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.875 178.402 4411 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.14 % Allowed : 12.07 % Favored : 86.79 % 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: 1.58 (0.25), residues: 1107 helix: 2.37 (0.20), residues: 671 sheet: 0.99 (0.65), residues: 52 loop : -1.45 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 364 TYR 0.021 0.002 TYR K 495 PHE 0.017 0.002 PHE C 25 TRP 0.043 0.004 TRP K 431 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00469 (15861) covalent geometry : angle 0.60185 (22634) hydrogen bonds : bond 0.06649 ( 860) hydrogen bonds : angle 2.76328 ( 2182) metal coordination : bond 0.01447 ( 4) metal coordination : angle 1.87504 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.18 seconds wall clock time: 53 minutes 5.20 seconds (3185.20 seconds total)