Starting phenix.real_space_refine on Fri Jul 3 14:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7joa_22409/07_2026/7joa_22409.cif Found real_map, /net/cci-nas-00/data/ceres_data/7joa_22409/07_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_22409/07_2026/7joa_22409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7joa_22409/07_2026/7joa_22409.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7joa_22409/07_2026/7joa_22409.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7joa_22409/07_2026/7joa_22409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7joa_22409/07_2026/7joa_22409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7joa_22409/07_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-6108/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: 3.30, 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: 1.17 Conformation dependent library (CDL) restraints added in 488.2 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: 2.09 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: 3.89 Time building geometry restraints manager: 1.64 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: 20708 1.61 - 3.21: 1789 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.680 Find NCS groups from input model: 0.110 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- 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= 0.712 Angle : 0.911 19.373 22637 Z= 0.720 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 / 0.69 (15861) covalent geometry : angle 0.89644 / 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 : 0.385 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: 0.1781 time to fit residues: 55.5513 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: 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: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 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 = 0.3862 r_free = 0.3862 target = 0.146110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107313 restraints weight = 24031.864| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.39 r_work: 0.2966 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1984 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= 0.185 Angle : 0.679 9.584 22637 Z= 0.391 Chirality : 0.048 0.242 2547 Planarity : 0.005 0.046 1861 Dihedral : 29.310 171.129 4411 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.75 % Allowed : 7.02 % Favored : 91.23 % 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: 2.11 (0.20), residues: 652 sheet: 0.12 (0.68), residues: 59 loop : -1.71 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 364 TYR 0.015 0.002 TYR K 346 PHE 0.024 0.003 PHE K 488 TRP 0.046 0.004 TRP K 431 HIS 0.005 0.002 HIS K 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (15861) covalent geometry : angle 0.67836 / 0.39 (22634) hydrogen bonds : bond 0.06813 / 4.66 ( 860) hydrogen bonds : angle 3.04392 / 2.10 ( 2182) metal coordination : bond 0.02354 / 1.20 ( 4) metal coordination : angle 2.61969 / 1.47 ( 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 169 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.400 Fit side-chains REVERT: C 61 GLU cc_start: 0.8268 (tp30) cc_final: 0.8032 (mm-30) REVERT: C 95 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8581 (tttm) REVERT: G 74 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7315 (mmmt) REVERT: G 91 GLU cc_start: 0.7202 (tt0) cc_final: 0.6986 (tt0) REVERT: G 95 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8627 (tttm) REVERT: K 183 GLN cc_start: 0.5972 (mt0) cc_final: 0.5673 (tm-30) REVERT: K 194 GLN cc_start: 0.5577 (tt0) cc_final: 0.4956 (pp30) REVERT: K 215 MET cc_start: 0.6931 (mmt) cc_final: 0.6640 (mmt) REVERT: K 273 GLU cc_start: 0.3511 (mm-30) cc_final: 0.3076 (mm-30) REVERT: K 496 GLU cc_start: 0.3112 (mm-30) cc_final: 0.2270 (mm-30) outliers start: 17 outliers final: 12 residues processed: 161 average time/residue: 0.1523 time to fit residues: 33.1447 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 : 0.395 ------------------------------------------------------------------------------- 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 E residue 58 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: 0.5980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.146605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107931 restraints weight = 24334.145| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.43 r_work: 0.2968 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2477 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= 0.140 Angle : 0.591 6.164 22637 Z= 0.345 Chirality : 0.044 0.225 2547 Planarity : 0.004 0.053 1861 Dihedral : 29.267 173.017 4411 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.75 % Allowed : 8.98 % Favored : 89.27 % 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: 1.63 (0.25), residues: 1107 helix: 2.58 (0.20), residues: 660 sheet: 0.46 (0.75), residues: 52 loop : -1.58 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 364 TYR 0.010 0.001 TYR K 346 PHE 0.053 0.002 PHE K 488 TRP 0.026 0.002 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (15861) covalent geometry : angle 0.58988 / 0.34 (22634) hydrogen bonds : bond 0.05685 / 3.90 ( 860) hydrogen bonds : angle 2.80669 / 1.94 ( 2182) metal coordination : bond 0.01426 / 0.74 ( 4) metal coordination : angle 2.61760 / 1.37 ( 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 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.407 Fit side-chains REVERT: C 61 GLU cc_start: 0.8330 (tp30) cc_final: 0.8059 (mm-30) REVERT: C 95 LYS cc_start: 0.9145 (ttmm) cc_final: 0.8598 (tttm) REVERT: G 74 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7371 (mmmt) REVERT: G 95 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8564 (tttm) REVERT: H 88 THR cc_start: 0.8955 (t) cc_final: 0.8711 (m) REVERT: K 194 GLN cc_start: 0.5659 (tt0) cc_final: 0.5100 (pp30) REVERT: K 215 MET cc_start: 0.6908 (mmt) cc_final: 0.6559 (mmt) REVERT: K 253 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6456 (pt0) REVERT: K 273 GLU cc_start: 0.3725 (mm-30) cc_final: 0.3131 (mm-30) REVERT: K 322 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7551 (p) REVERT: K 396 GLU cc_start: 0.6629 (mp0) cc_final: 0.6203 (mp0) outliers start: 17 outliers final: 11 residues processed: 157 average time/residue: 0.1537 time to fit residues: 32.7901 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 G residue 114 VAL Chi-restraints excluded: chain H residue 90 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: 0.3980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.147046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107678 restraints weight = 23982.638| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.39 r_work: 0.2978 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15865 Z= 0.132 Angle : 0.573 10.848 22637 Z= 0.334 Chirality : 0.043 0.228 2547 Planarity : 0.004 0.037 1861 Dihedral : 29.203 172.840 4411 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.75 % Allowed : 9.91 % Favored : 88.34 % 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: 1.81 (0.25), residues: 1107 helix: 2.69 (0.20), residues: 662 sheet: 0.59 (0.75), residues: 52 loop : -1.48 (0.27), residues: 393 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 0.050 0.002 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 0.00218 / 0.13 (15861) covalent geometry : angle 0.57244 / 0.33 (22634) hydrogen bonds : bond 0.05155 / 3.54 ( 860) hydrogen bonds : angle 2.68471 / 1.85 ( 2182) metal coordination : bond 0.00622 / 0.32 ( 4) metal coordination : angle 1.79441 / 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 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.259 Fit side-chains REVERT: C 95 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8638 (tttm) REVERT: D 63 ASN cc_start: 0.8461 (t0) cc_final: 0.8126 (m-40) REVERT: G 74 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7341 (mmmt) REVERT: G 95 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8592 (tttm) REVERT: K 194 GLN cc_start: 0.5738 (tt0) cc_final: 0.5449 (tm-30) REVERT: K 215 MET cc_start: 0.6977 (mmt) cc_final: 0.6755 (mmt) REVERT: K 273 GLU cc_start: 0.3787 (mm-30) cc_final: 0.3089 (mm-30) REVERT: K 326 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6805 (tt) REVERT: K 482 ASP cc_start: 0.3317 (t0) cc_final: 0.2602 (m-30) REVERT: K 496 GLU cc_start: 0.3240 (mm-30) cc_final: 0.2344 (mm-30) outliers start: 17 outliers final: 15 residues processed: 142 average time/residue: 0.1515 time to fit residues: 29.1851 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 108 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103677 restraints weight = 23827.682| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.54 r_work: 0.2922 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15865 Z= 0.146 Angle : 0.582 10.241 22637 Z= 0.334 Chirality : 0.044 0.224 2547 Planarity : 0.004 0.035 1861 Dihedral : 29.285 174.300 4411 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 10.84 % Favored : 87.51 % 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: 2.72 (0.20), residues: 663 sheet: 0.56 (0.73), residues: 52 loop : -1.50 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 364 TYR 0.010 0.001 TYR K 346 PHE 0.033 0.002 PHE K 488 TRP 0.038 0.003 TRP K 431 HIS 0.004 0.001 HIS K 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (15861) covalent geometry : angle 0.58207 / 0.33 (22634) hydrogen bonds : bond 0.05661 / 3.88 ( 860) hydrogen bonds : angle 2.67643 / 1.86 ( 2182) metal coordination : bond 0.01503 / 0.79 ( 4) metal coordination : angle 1.27985 / 0.69 ( 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 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.418 Fit side-chains REVERT: C 95 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8644 (tttm) REVERT: D 63 ASN cc_start: 0.8524 (t0) cc_final: 0.8163 (m-40) REVERT: G 74 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7433 (mmmt) REVERT: G 95 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8569 (tttm) REVERT: K 194 GLN cc_start: 0.5962 (tt0) cc_final: 0.5636 (tm-30) REVERT: K 215 MET cc_start: 0.6937 (mmt) cc_final: 0.6715 (mmt) REVERT: K 273 GLU cc_start: 0.3826 (mm-30) cc_final: 0.3143 (mm-30) REVERT: K 322 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7615 (p) REVERT: K 396 GLU cc_start: 0.6452 (mp0) cc_final: 0.6031 (mp0) REVERT: K 482 ASP cc_start: 0.3226 (t0) cc_final: 0.2585 (m-30) REVERT: K 496 GLU cc_start: 0.3522 (mm-30) cc_final: 0.2772 (mm-30) outliers start: 16 outliers final: 13 residues processed: 145 average time/residue: 0.1578 time to fit residues: 31.0575 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 74 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.146104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103811 restraints weight = 23861.218| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.45 r_work: 0.2937 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3208 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= 0.134 Angle : 0.560 8.442 22637 Z= 0.324 Chirality : 0.042 0.226 2547 Planarity : 0.004 0.035 1861 Dihedral : 29.233 174.408 4411 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.55 % Allowed : 11.97 % Favored : 86.48 % 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: 1.93 (0.25), residues: 1107 helix: 2.78 (0.20), residues: 661 sheet: 0.62 (0.71), residues: 52 loop : -1.40 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 241 TYR 0.009 0.001 TYR K 346 PHE 0.027 0.002 PHE K 488 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 0.00239 / 0.13 (15861) covalent geometry : angle 0.55963 / 0.32 (22634) hydrogen bonds : bond 0.05285 / 3.64 ( 860) hydrogen bonds : angle 2.60678 / 1.82 ( 2182) metal coordination : bond 0.00788 / 0.41 ( 4) metal coordination : angle 1.96341 / 1.04 ( 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 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.425 Fit side-chains REVERT: C 95 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8634 (tttm) REVERT: D 63 ASN cc_start: 0.8466 (t0) cc_final: 0.8161 (m-40) REVERT: G 74 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7406 (mmmt) REVERT: G 95 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8551 (tttm) REVERT: H 68 ASP cc_start: 0.8571 (t0) cc_final: 0.8282 (t0) REVERT: K 194 GLN cc_start: 0.6082 (tt0) cc_final: 0.5764 (tm-30) REVERT: K 215 MET cc_start: 0.6946 (mmt) cc_final: 0.6736 (mmt) REVERT: K 273 GLU cc_start: 0.3788 (mm-30) cc_final: 0.3079 (mm-30) REVERT: K 322 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7640 (p) REVERT: K 396 GLU cc_start: 0.6418 (mp0) cc_final: 0.5971 (mp0) REVERT: K 482 ASP cc_start: 0.3220 (t0) cc_final: 0.2531 (m-30) REVERT: K 492 LYS cc_start: 0.2312 (OUTLIER) cc_final: 0.2086 (pttp) REVERT: K 496 GLU cc_start: 0.3656 (mm-30) cc_final: 0.2991 (mm-30) outliers start: 15 outliers final: 12 residues processed: 140 average time/residue: 0.1666 time to fit residues: 31.5258 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain K residue 492 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103631 restraints weight = 23610.033| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.43 r_work: 0.2955 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15865 Z= 0.138 Angle : 0.562 7.619 22637 Z= 0.325 Chirality : 0.043 0.225 2547 Planarity : 0.004 0.036 1861 Dihedral : 29.245 175.271 4411 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.96 % Allowed : 11.97 % Favored : 86.07 % 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: 1.98 (0.25), residues: 1107 helix: 2.81 (0.20), residues: 661 sheet: 0.69 (0.71), residues: 52 loop : -1.37 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 483 TYR 0.010 0.001 TYR K 346 PHE 0.013 0.002 PHE K 449 TRP 0.019 0.002 TRP K 431 HIS 0.004 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15861) covalent geometry : angle 0.56124 / 0.33 (22634) hydrogen bonds : bond 0.05424 / 3.73 ( 860) hydrogen bonds : angle 2.60795 / 1.82 ( 2182) metal coordination : bond 0.00786 / 0.41 ( 4) metal coordination : angle 1.69032 / 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 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.424 Fit side-chains REVERT: C 95 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8667 (tttm) REVERT: D 33 ARG cc_start: 0.7482 (ptt180) cc_final: 0.7214 (ptt180) REVERT: G 74 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7331 (mmmt) REVERT: G 95 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8526 (tttm) REVERT: K 215 MET cc_start: 0.6846 (mmt) cc_final: 0.6614 (mmt) REVERT: K 273 GLU cc_start: 0.3764 (mm-30) cc_final: 0.3069 (mm-30) REVERT: K 322 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7662 (p) REVERT: K 396 GLU cc_start: 0.6401 (mp0) cc_final: 0.5953 (mp0) REVERT: K 482 ASP cc_start: 0.3209 (t0) cc_final: 0.2506 (m-30) REVERT: K 492 LYS cc_start: 0.2232 (OUTLIER) cc_final: 0.2014 (pttp) REVERT: K 496 GLU cc_start: 0.3767 (mm-30) cc_final: 0.3130 (mm-30) outliers start: 19 outliers final: 15 residues processed: 137 average time/residue: 0.1615 time to fit residues: 30.2702 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 457 LEU Chi-restraints excluded: chain K residue 492 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 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: 0.1980 chunk 134 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.146534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107091 restraints weight = 23986.722| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.25 r_work: 0.2980 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15865 Z= 0.145 Angle : 0.570 7.723 22637 Z= 0.328 Chirality : 0.043 0.224 2547 Planarity : 0.004 0.034 1861 Dihedral : 29.232 175.850 4411 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.96 % Allowed : 12.07 % Favored : 85.96 % 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: 2.81 (0.20), residues: 662 sheet: 0.73 (0.69), residues: 52 loop : -1.31 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 364 TYR 0.012 0.001 TYR K 346 PHE 0.014 0.002 PHE C 25 TRP 0.021 0.002 TRP K 431 HIS 0.003 0.001 HIS K 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (15861) covalent geometry : angle 0.56936 / 0.33 (22634) hydrogen bonds : bond 0.05650 / 3.89 ( 860) hydrogen bonds : angle 2.61587 / 1.83 ( 2182) metal coordination : bond 0.00786 / 0.41 ( 4) metal coordination : angle 1.85081 / 0.98 ( 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 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.356 Fit side-chains REVERT: C 95 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8678 (tttm) REVERT: D 33 ARG cc_start: 0.7549 (ptt180) cc_final: 0.7267 (ptt180) REVERT: G 74 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7419 (mmmt) REVERT: G 95 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8544 (tttm) REVERT: K 194 GLN cc_start: 0.6000 (tt0) cc_final: 0.5655 (tp40) REVERT: K 273 GLU cc_start: 0.3741 (mm-30) cc_final: 0.2748 (mt-10) REVERT: K 322 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7688 (p) REVERT: K 396 GLU cc_start: 0.6483 (mp0) cc_final: 0.6032 (mp0) REVERT: K 482 ASP cc_start: 0.3246 (t0) cc_final: 0.2546 (m-30) REVERT: K 496 GLU cc_start: 0.3680 (mm-30) cc_final: 0.2926 (mm-30) outliers start: 19 outliers final: 16 residues processed: 138 average time/residue: 0.1537 time to fit residues: 28.9615 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 108 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.144342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104427 restraints weight = 23895.746| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.23 r_work: 0.2942 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15865 Z= 0.195 Angle : 0.646 10.354 22637 Z= 0.361 Chirality : 0.047 0.222 2547 Planarity : 0.005 0.039 1861 Dihedral : 29.324 177.668 4411 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.44 % Allowed : 13.21 % Favored : 85.35 % 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: 1.77 (0.25), residues: 1107 helix: 2.57 (0.20), residues: 663 sheet: 0.76 (0.68), residues: 52 loop : -1.34 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 364 TYR 0.015 0.002 TYR K 346 PHE 0.021 0.002 PHE C 25 TRP 0.028 0.003 TRP K 431 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (15861) covalent geometry : angle 0.64568 / 0.36 (22634) hydrogen bonds : bond 0.06897 / 4.72 ( 860) hydrogen bonds : angle 2.78226 / 1.96 ( 2182) metal coordination : bond 0.01158 / 0.61 ( 4) metal coordination : angle 2.07037 / 1.09 ( 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 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.349 Fit side-chains REVERT: C 95 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8659 (tttm) REVERT: D 33 ARG cc_start: 0.7619 (ptt180) cc_final: 0.7389 (ptt180) REVERT: E 56 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8806 (tttp) REVERT: G 74 LYS cc_start: 0.8410 (mtmm) cc_final: 0.7584 (mmmt) REVERT: G 95 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8542 (tttm) REVERT: K 273 GLU cc_start: 0.3685 (mm-30) cc_final: 0.3053 (mm-30) REVERT: K 322 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7727 (p) REVERT: K 396 GLU cc_start: 0.6425 (mp0) cc_final: 0.5961 (mp0) REVERT: K 482 ASP cc_start: 0.3262 (t0) cc_final: 0.2671 (m-30) outliers start: 14 outliers final: 13 residues processed: 126 average time/residue: 0.1490 time to fit residues: 25.9322 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.145362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105317 restraints weight = 23857.586| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.22 r_work: 0.2964 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15865 Z= 0.146 Angle : 0.607 9.101 22637 Z= 0.344 Chirality : 0.045 0.225 2547 Planarity : 0.004 0.034 1861 Dihedral : 29.282 176.693 4411 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.65 % Allowed : 13.11 % Favored : 85.24 % 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: 2.65 (0.20), residues: 664 sheet: 0.81 (0.68), residues: 52 loop : -1.34 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 364 TYR 0.012 0.001 TYR K 346 PHE 0.013 0.002 PHE C 25 TRP 0.034 0.003 TRP K 431 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (15861) covalent geometry : angle 0.60702 / 0.34 (22634) hydrogen bonds : bond 0.06202 / 4.26 ( 860) hydrogen bonds : angle 2.71490 / 1.91 ( 2182) metal coordination : bond 0.00934 / 0.49 ( 4) metal coordination : angle 1.90428 / 1.00 ( 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 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.431 Fit side-chains REVERT: C 95 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8648 (tttm) REVERT: D 33 ARG cc_start: 0.7606 (ptt180) cc_final: 0.7355 (ptt180) REVERT: G 74 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7476 (mmmt) REVERT: G 95 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8563 (tttm) REVERT: K 273 GLU cc_start: 0.3647 (mm-30) cc_final: 0.2667 (mt-10) REVERT: K 322 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7705 (p) REVERT: K 396 GLU cc_start: 0.6411 (mp0) cc_final: 0.5948 (mp0) REVERT: K 482 ASP cc_start: 0.3179 (t0) cc_final: 0.2628 (m-30) outliers start: 16 outliers final: 15 residues processed: 126 average time/residue: 0.1392 time to fit residues: 24.3281 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 80 THR 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 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 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: 10.0000 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101919 restraints weight = 23893.297| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.58 r_work: 0.2880 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15865 Z= 0.179 Angle : 0.625 8.501 22637 Z= 0.352 Chirality : 0.046 0.222 2547 Planarity : 0.004 0.038 1861 Dihedral : 29.294 177.471 4411 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.55 % Allowed : 13.31 % Favored : 85.14 % 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: 1.76 (0.25), residues: 1107 helix: 2.56 (0.20), residues: 664 sheet: 0.74 (0.66), residues: 52 loop : -1.36 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 497 TYR 0.014 0.002 TYR K 346 PHE 0.018 0.002 PHE C 25 TRP 0.035 0.003 TRP K 431 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (15861) covalent geometry : angle 0.62493 / 0.35 (22634) hydrogen bonds : bond 0.06530 / 4.48 ( 860) hydrogen bonds : angle 2.73292 / 1.92 ( 2182) metal coordination : bond 0.01157 / 0.61 ( 4) metal coordination : angle 1.96069 / 1.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.51 seconds wall clock time: 52 minutes 6.70 seconds (3126.70 seconds total)