Starting phenix.real_space_refine on Sat Sep 12 07:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jo9_22408/09_2026/7jo9_22408.cif" } 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 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14994 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2960 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13969 SG CYS K 384 40.430 21.150 77.314 1.00 84.47 S ATOM 13975 SG CYS K 385 36.531 21.814 76.213 1.00 87.46 S ATOM 14020 SG CYS K 392 36.749 21.709 79.807 1.00 89.32 S Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 14994 At special positions: 0 Unit cell: (121.03, 135.59, 125.58, 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 395.4 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=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " 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 63.0% alpha, 7.4% beta 138 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.512A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.530A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.670A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.219A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.500A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.863A 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 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.610A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.043A 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: 3.739A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.703A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.109A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.020A 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: 3.977A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.596A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.611A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.575A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.102A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.583A 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 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.611A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.043A 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: 3.739A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.703A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.109A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 185 removed outlier: 4.019A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE K 164 " --> pdb=" O LYS K 160 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 5.309A 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: 3.741A pdb=" N GLU K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 removed outlier: 4.400A pdb=" N GLU K 324 " --> pdb=" O SER K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 342 removed outlier: 3.535A 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: 3.999A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 4.028A 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 Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 501 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.137A 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 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: 7.629A 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: 6.957A 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: 7.489A 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 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.767A 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: 4.619A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 4.083A 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: 4.619A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.687A 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 253 511 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 1.43 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: 3006 1.33 - 1.45: 4768 1.45 - 1.57: 7469 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 1.389 0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C3' DA J -25 " pdb=" O3' DA J -25 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" C3' DC I 61 " pdb=" C2' DC I 61 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 bond pdb=" C3' DA I -68 " pdb=" C2' DA I -68 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C3' DA I -14 " pdb=" O3' DA I -14 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.53e+00 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 20811 1.59 - 3.17: 1701 3.17 - 4.76: 93 4.76 - 6.35: 21 6.35 - 7.93: 8 Bond angle restraints: 22634 Sorted by residual: angle pdb=" O4' DA J 32 " pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" O4' DC I -25 " pdb=" C1' DC I -25 " pdb=" N1 DC I -25 " ideal model delta sigma weight residual 108.00 111.17 -3.17 7.00e-01 2.04e+00 2.06e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " 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 - 33.52: 7314 33.52 - 67.04: 1488 67.04 - 100.56: 40 100.56 - 134.08: 0 134.08 - 167.60: 1 Dihedral angle restraints: 8843 sinusoidal: 5568 harmonic: 3275 Sorted by residual: dihedral pdb=" CA ARG H 33 " pdb=" C ARG H 33 " pdb=" N LYS H 34 " pdb=" CA LYS H 34 " ideal model delta harmonic sigma weight residual 180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ARG D 33 " pdb=" C ARG D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 52.40 167.60 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1246 0.030 - 0.059: 746 0.059 - 0.089: 356 0.089 - 0.119: 154 0.119 - 0.148: 45 Chirality restraints: 2547 Sorted by residual: chirality pdb=" C3' DC I 52 " pdb=" C4' DC I 52 " pdb=" O3' DC I 52 " pdb=" C2' DC I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 2544 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER K 446 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C SER K 446 " -0.055 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 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 454 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C ALA K 454 " 0.053 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 447 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C SER K 447 " 0.051 2.00e-02 2.50e+03 pdb=" O SER K 447 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS K 448 " -0.017 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2251 2.76 - 3.29: 13369 3.29 - 3.83: 26368 3.83 - 4.36: 30229 4.36 - 4.90: 45966 Nonbonded interactions: 118183 Sorted by model distance: nonbonded pdb=" OE1 GLU C 64 " pdb=" NH2 ARG K 222 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR K 421 " pdb=" NE2 HIS K 467 " model vdw 2.237 3.120 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.255 3.120 nonbonded pdb=" NH2 ARG F 19 " pdb=" OP1 DA J -22 " model vdw 2.276 3.120 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.289 3.120 ... (remaining 118178 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: 2.370 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.437 15865 Z= 0.663 Angle : 0.866 7.933 22637 Z= 0.699 Chirality : 0.049 0.148 2547 Planarity : 0.005 0.067 1861 Dihedral : 25.947 167.599 6725 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.41 % Allowed : 0.72 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1107 helix: 1.48 (0.20), residues: 646 sheet: -0.28 (0.64), residues: 57 loop : -1.83 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 443 TYR 0.023 0.002 TYR K 346 PHE 0.023 0.002 PHE K 266 TRP 0.014 0.002 TRP K 363 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.64 (15861) covalent geometry : angle 0.86304 / 0.70 (22634) hydrogen bonds : bond 0.11259 / 7.98 ( 864) hydrogen bonds : angle 4.29722 / 3.12 ( 2194) metal coordination : bond 0.26951 / 13.06 ( 4) metal coordination : angle 5.96912 / 3.16 ( 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 235 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.448 Fit side-chains REVERT: D 68 ASP cc_start: 0.8115 (t0) cc_final: 0.7911 (t0) REVERT: E 73 GLU cc_start: 0.8100 (tt0) cc_final: 0.7668 (tt0) REVERT: E 90 MET cc_start: 0.7432 (mmp) cc_final: 0.7133 (mmm) REVERT: F 68 ASP cc_start: 0.7764 (m-30) cc_final: 0.7555 (m-30) REVERT: F 91 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8157 (ttmm) REVERT: G 99 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8074 (mmtt) REVERT: K 173 LYS cc_start: 0.5271 (mtmm) cc_final: 0.5068 (mtmt) REVERT: K 269 ILE cc_start: 0.6058 (mt) cc_final: 0.5368 (tt) outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.1811 time to fit residues: 55.6700 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS D 63 ASN E 68 GLN G 38 ASN H 47 GLN K 339 ASN K 429 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116317 restraints weight = 22319.907| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.49 r_work: 0.2915 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15865 Z= 0.166 Angle : 0.660 7.177 22637 Z= 0.380 Chirality : 0.047 0.250 2547 Planarity : 0.005 0.064 1861 Dihedral : 29.065 169.102 4411 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.14 % Allowed : 8.46 % Favored : 90.40 % 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: 1.41 (0.25), residues: 1107 helix: 2.29 (0.20), residues: 654 sheet: 0.34 (0.66), residues: 58 loop : -1.40 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 20 TYR 0.019 0.002 TYR H 83 PHE 0.020 0.002 PHE K 455 TRP 0.011 0.001 TRP K 363 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (15861) covalent geometry : angle 0.65941 / 0.38 (22634) hydrogen bonds : bond 0.06663 / 4.58 ( 864) hydrogen bonds : angle 3.08131 / 2.26 ( 2194) metal coordination : bond 0.01895 / 0.92 ( 4) metal coordination : angle 2.96040 / 1.60 ( 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 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8436 (t0) cc_final: 0.7994 (t70) REVERT: E 90 MET cc_start: 0.8151 (mmp) cc_final: 0.7873 (mmm) REVERT: E 123 ASP cc_start: 0.8744 (m-30) cc_final: 0.8501 (m-30) REVERT: F 91 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8618 (tttt) REVERT: G 99 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8438 (mmmt) REVERT: K 173 LYS cc_start: 0.5289 (mtmm) cc_final: 0.5013 (mtmt) REVERT: K 180 ARG cc_start: 0.4842 (tpm170) cc_final: 0.3955 (mtm-85) REVERT: K 353 LYS cc_start: 0.3486 (mmpt) cc_final: 0.2735 (pttm) REVERT: K 496 GLU cc_start: 0.5551 (mm-30) cc_final: 0.5296 (tp30) outliers start: 11 outliers final: 5 residues processed: 150 average time/residue: 0.1663 time to fit residues: 34.0723 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 123 optimal weight: 0.0030 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN G 38 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115045 restraints weight = 22357.018| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.41 r_work: 0.2913 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15865 Z= 0.137 Angle : 0.588 6.328 22637 Z= 0.345 Chirality : 0.044 0.253 2547 Planarity : 0.004 0.047 1861 Dihedral : 29.019 171.098 4411 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.14 % Allowed : 9.29 % Favored : 89.58 % 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: 1.79 (0.26), residues: 1107 helix: 2.54 (0.20), residues: 660 sheet: 0.53 (0.68), residues: 58 loop : -1.21 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.016 0.001 TYR K 373 PHE 0.011 0.001 PHE K 455 TRP 0.008 0.001 TRP K 363 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (15861) covalent geometry : angle 0.58689 / 0.35 (22634) hydrogen bonds : bond 0.05636 / 3.88 ( 864) hydrogen bonds : angle 2.88660 / 2.10 ( 2194) metal coordination : bond 0.00783 / 0.38 ( 4) metal coordination : angle 2.74146 / 1.44 ( 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 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8500 (t0) cc_final: 0.8063 (t70) REVERT: E 90 MET cc_start: 0.8087 (mmp) cc_final: 0.7831 (mmm) REVERT: E 123 ASP cc_start: 0.8788 (m-30) cc_final: 0.8588 (m-30) REVERT: F 91 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8646 (tttt) REVERT: G 99 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8396 (mmmt) REVERT: K 173 LYS cc_start: 0.5202 (mtmm) cc_final: 0.4979 (mtmt) REVERT: K 269 ILE cc_start: 0.5699 (mt) cc_final: 0.5407 (tt) REVERT: K 353 LYS cc_start: 0.3523 (mmpt) cc_final: 0.2756 (pttm) REVERT: K 496 GLU cc_start: 0.5719 (mm-30) cc_final: 0.5100 (tp30) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 0.1620 time to fit residues: 31.9474 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN F 75 HIS G 38 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.150879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111393 restraints weight = 22157.420| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.47 r_work: 0.2901 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15865 Z= 0.151 Angle : 0.596 5.948 22637 Z= 0.345 Chirality : 0.045 0.250 2547 Planarity : 0.004 0.048 1861 Dihedral : 29.046 172.268 4411 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.55 % Allowed : 10.84 % Favored : 87.62 % 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: 1.89 (0.26), residues: 1107 helix: 2.61 (0.20), residues: 662 sheet: 0.59 (0.68), residues: 58 loop : -1.16 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.018 0.002 TYR K 373 PHE 0.016 0.002 PHE G 25 TRP 0.008 0.001 TRP K 363 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (15861) covalent geometry : angle 0.59586 / 0.34 (22634) hydrogen bonds : bond 0.06040 / 4.15 ( 864) hydrogen bonds : angle 2.81390 / 2.04 ( 2194) metal coordination : bond 0.00562 / 0.29 ( 4) metal coordination : angle 2.37224 / 1.25 ( 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 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: D 33 ARG cc_start: 0.7220 (ppt170) cc_final: 0.6894 (ptt180) REVERT: D 68 ASP cc_start: 0.8469 (t0) cc_final: 0.8096 (t70) REVERT: E 90 MET cc_start: 0.8243 (mmp) cc_final: 0.7983 (mmm) REVERT: F 91 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8676 (tttt) REVERT: G 99 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8534 (mmmt) REVERT: K 173 LYS cc_start: 0.5145 (mtmm) cc_final: 0.4793 (mtmt) REVERT: K 472 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6673 (ptpp) REVERT: K 496 GLU cc_start: 0.5603 (mm-30) cc_final: 0.4915 (tp30) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.1618 time to fit residues: 30.2075 Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 472 LYS Chi-restraints excluded: chain K residue 481 ILE 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: 7.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN E 76 GLN F 25 ASN G 38 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112073 restraints weight = 22141.233| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.45 r_work: 0.2917 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15865 Z= 0.142 Angle : 0.580 6.686 22637 Z= 0.336 Chirality : 0.044 0.254 2547 Planarity : 0.004 0.044 1861 Dihedral : 29.035 173.281 4411 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.55 % Allowed : 12.07 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1107 helix: 2.68 (0.20), residues: 663 sheet: 0.58 (0.69), residues: 58 loop : -1.14 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.017 0.001 TYR K 373 PHE 0.018 0.002 PHE K 449 TRP 0.007 0.001 TRP K 363 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (15861) covalent geometry : angle 0.57927 / 0.34 (22634) hydrogen bonds : bond 0.05714 / 3.93 ( 864) hydrogen bonds : angle 2.75577 / 2.00 ( 2194) metal coordination : bond 0.00441 / 0.22 ( 4) metal coordination : angle 2.23791 / 1.17 ( 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 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.421 Fit side-chains REVERT: D 33 ARG cc_start: 0.7212 (ppt170) cc_final: 0.6996 (ptt180) REVERT: D 68 ASP cc_start: 0.8486 (t0) cc_final: 0.8110 (t70) REVERT: E 90 MET cc_start: 0.8110 (mmp) cc_final: 0.7877 (mmm) REVERT: F 91 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8614 (ttmm) REVERT: G 99 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8558 (mmmt) REVERT: K 154 LEU cc_start: 0.3453 (OUTLIER) cc_final: 0.3000 (tt) REVERT: K 173 LYS cc_start: 0.5028 (mtmm) cc_final: 0.4705 (mtmt) REVERT: K 180 ARG cc_start: 0.4572 (tpm170) cc_final: 0.3861 (mtm-85) REVERT: K 269 ILE cc_start: 0.5604 (mt) cc_final: 0.5349 (tt) REVERT: K 430 MET cc_start: 0.7129 (mmm) cc_final: 0.6866 (mmp) REVERT: K 455 PHE cc_start: 0.5819 (t80) cc_final: 0.5600 (t80) REVERT: K 472 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6643 (ptpp) REVERT: K 496 GLU cc_start: 0.5361 (mm-30) cc_final: 0.4666 (tp30) outliers start: 15 outliers final: 7 residues processed: 132 average time/residue: 0.1601 time to fit residues: 28.9517 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 472 LYS Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN G 104 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109060 restraints weight = 21985.434| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.42 r_work: 0.2796 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15865 Z= 0.209 Angle : 0.685 6.544 22637 Z= 0.381 Chirality : 0.050 0.250 2547 Planarity : 0.005 0.048 1861 Dihedral : 29.247 174.535 4411 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.17 % Allowed : 11.97 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1107 helix: 2.24 (0.20), residues: 663 sheet: 0.26 (0.70), residues: 60 loop : -1.29 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.018 0.002 TYR K 373 PHE 0.029 0.003 PHE C 25 TRP 0.020 0.003 TRP K 431 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (15861) covalent geometry : angle 0.68471 / 0.38 (22634) hydrogen bonds : bond 0.07684 / 5.26 ( 864) hydrogen bonds : angle 2.95047 / 2.14 ( 2194) metal coordination : bond 0.01722 / 0.85 ( 4) metal coordination : angle 1.79329 / 0.96 ( 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 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.438 Fit side-chains REVERT: D 33 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7156 (ptt180) REVERT: D 68 ASP cc_start: 0.8587 (t0) cc_final: 0.8361 (t0) REVERT: E 90 MET cc_start: 0.8545 (mmp) cc_final: 0.8263 (mmm) REVERT: F 91 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8637 (ttmm) REVERT: G 99 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8663 (mmmt) REVERT: K 154 LEU cc_start: 0.3486 (OUTLIER) cc_final: 0.3046 (tt) REVERT: K 173 LYS cc_start: 0.5123 (mtmm) cc_final: 0.4770 (mtmt) REVERT: K 180 ARG cc_start: 0.4559 (tpm170) cc_final: 0.3678 (mtm-85) REVERT: K 430 MET cc_start: 0.7154 (mmm) cc_final: 0.6938 (mmp) REVERT: K 431 TRP cc_start: 0.7503 (m-10) cc_final: 0.7230 (m-10) REVERT: K 472 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6770 (ptpp) REVERT: K 496 GLU cc_start: 0.5686 (mm-30) cc_final: 0.5187 (tp30) outliers start: 21 outliers final: 11 residues processed: 144 average time/residue: 0.1611 time to fit residues: 32.0149 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 472 LYS Chi-restraints excluded: chain K residue 481 ILE 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: 0.6980 chunk 12 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.150109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111678 restraints weight = 22051.748| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.31 r_work: 0.2853 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15865 Z= 0.139 Angle : 0.622 9.027 22637 Z= 0.351 Chirality : 0.047 0.256 2547 Planarity : 0.004 0.062 1861 Dihedral : 29.185 174.577 4411 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.86 % Allowed : 12.90 % 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: 1.67 (0.25), residues: 1107 helix: 2.43 (0.20), residues: 663 sheet: 0.36 (0.70), residues: 60 loop : -1.24 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 42 TYR 0.018 0.001 TYR K 373 PHE 0.023 0.002 PHE K 449 TRP 0.014 0.002 TRP K 431 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (15861) covalent geometry : angle 0.62146 / 0.35 (22634) hydrogen bonds : bond 0.06314 / 4.34 ( 864) hydrogen bonds : angle 2.90874 / 2.10 ( 2194) metal coordination : bond 0.00457 / 0.23 ( 4) metal coordination : angle 2.28769 / 1.21 ( 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 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.462 Fit side-chains REVERT: E 90 MET cc_start: 0.8302 (mmp) cc_final: 0.8041 (mmm) REVERT: F 91 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8525 (ttmm) REVERT: G 99 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8552 (mmmt) REVERT: K 173 LYS cc_start: 0.5117 (mtmm) cc_final: 0.4777 (mtmt) REVERT: K 373 TYR cc_start: 0.6224 (t80) cc_final: 0.5666 (t80) REVERT: K 430 MET cc_start: 0.7194 (mmm) cc_final: 0.6895 (mmp) REVERT: K 496 GLU cc_start: 0.5538 (mm-30) cc_final: 0.5089 (tp30) outliers start: 18 outliers final: 9 residues processed: 136 average time/residue: 0.1694 time to fit residues: 31.5951 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 499 ASN 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: 0.0570 chunk 82 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.151569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113409 restraints weight = 22317.949| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.32 r_work: 0.2886 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15865 Z= 0.130 Angle : 0.583 7.226 22637 Z= 0.334 Chirality : 0.044 0.260 2547 Planarity : 0.004 0.059 1861 Dihedral : 29.103 175.028 4411 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.03 % Allowed : 13.52 % Favored : 85.45 % 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: 1.92 (0.26), residues: 1107 helix: 2.65 (0.20), residues: 662 sheet: 0.44 (0.70), residues: 60 loop : -1.14 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 42 TYR 0.015 0.001 TYR K 373 PHE 0.009 0.001 PHE K 455 TRP 0.020 0.002 TRP K 431 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (15861) covalent geometry : angle 0.58225 / 0.33 (22634) hydrogen bonds : bond 0.05590 / 3.85 ( 864) hydrogen bonds : angle 2.77220 / 2.00 ( 2194) metal coordination : bond 0.00285 / 0.14 ( 4) metal coordination : angle 1.85189 / 0.97 ( 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 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.449 Fit side-chains REVERT: A 73 GLU cc_start: 0.8734 (tt0) cc_final: 0.8448 (tt0) REVERT: E 90 MET cc_start: 0.8101 (mmp) cc_final: 0.7859 (mmm) REVERT: F 91 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8519 (ttmm) REVERT: G 99 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8536 (mmmt) REVERT: K 180 ARG cc_start: 0.4624 (tpm170) cc_final: 0.3841 (mtm-85) REVERT: K 373 TYR cc_start: 0.6319 (t80) cc_final: 0.5714 (t80) REVERT: K 430 MET cc_start: 0.7137 (mmm) cc_final: 0.6885 (mmp) REVERT: K 455 PHE cc_start: 0.5777 (t80) cc_final: 0.5490 (t80) REVERT: K 496 GLU cc_start: 0.5566 (mm-30) cc_final: 0.5076 (tp30) outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 0.1586 time to fit residues: 29.1156 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.151898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114254 restraints weight = 22376.621| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.41 r_work: 0.2877 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15865 Z= 0.136 Angle : 0.578 7.275 22637 Z= 0.331 Chirality : 0.043 0.259 2547 Planarity : 0.004 0.063 1861 Dihedral : 29.100 175.076 4411 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.83 % Allowed : 14.14 % Favored : 85.04 % 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: 2.71 (0.20), residues: 658 sheet: 0.50 (0.69), residues: 60 loop : -1.11 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 42 TYR 0.014 0.001 TYR K 373 PHE 0.012 0.001 PHE C 25 TRP 0.013 0.001 TRP K 431 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (15861) covalent geometry : angle 0.57758 / 0.33 (22634) hydrogen bonds : bond 0.05568 / 3.83 ( 864) hydrogen bonds : angle 2.75118 / 1.98 ( 2194) metal coordination : bond 0.00308 / 0.15 ( 4) metal coordination : angle 1.88818 / 0.98 ( 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 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8153 (mtp180) REVERT: E 90 MET cc_start: 0.8105 (mmp) cc_final: 0.7873 (mmm) REVERT: F 91 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8573 (ttmm) REVERT: G 99 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8570 (mmmt) REVERT: K 180 ARG cc_start: 0.4532 (tpm170) cc_final: 0.3823 (mtm-85) REVERT: K 373 TYR cc_start: 0.6192 (t80) cc_final: 0.5637 (t80) REVERT: K 430 MET cc_start: 0.7207 (mmm) cc_final: 0.6935 (mmp) REVERT: K 496 GLU cc_start: 0.5533 (mm-30) cc_final: 0.5020 (tp30) outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.1668 time to fit residues: 28.8169 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN K 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112267 restraints weight = 22236.132| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.46 r_work: 0.2856 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15865 Z= 0.159 Angle : 0.604 6.276 22637 Z= 0.342 Chirality : 0.045 0.259 2547 Planarity : 0.004 0.064 1861 Dihedral : 29.160 175.188 4411 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.83 % Allowed : 14.14 % Favored : 85.04 % 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: 2.55 (0.20), residues: 661 sheet: 0.46 (0.68), residues: 60 loop : -1.19 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 42 TYR 0.014 0.001 TYR K 373 PHE 0.018 0.002 PHE K 449 TRP 0.008 0.001 TRP K 431 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (15861) covalent geometry : angle 0.60357 / 0.34 (22634) hydrogen bonds : bond 0.06275 / 4.32 ( 864) hydrogen bonds : angle 2.80102 / 2.02 ( 2194) metal coordination : bond 0.00339 / 0.17 ( 4) metal coordination : angle 1.75395 / 0.93 ( 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: 8 poor density : 124 time to evaluate : 0.445 Fit side-chains REVERT: E 90 MET cc_start: 0.8269 (mmp) cc_final: 0.8033 (mmm) REVERT: F 91 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8602 (ttmm) REVERT: G 99 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8578 (mmmt) REVERT: K 180 ARG cc_start: 0.4548 (tpm170) cc_final: 0.3824 (mtm-85) REVERT: K 496 GLU cc_start: 0.5459 (mm-30) cc_final: 0.5063 (tp30) outliers start: 8 outliers final: 8 residues processed: 131 average time/residue: 0.1697 time to fit residues: 30.4038 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE 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: 0.6980 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 24 optimal weight: 0.0270 chunk 59 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.151394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113558 restraints weight = 22158.862| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.33 r_work: 0.2885 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15865 Z= 0.129 Angle : 0.592 12.115 22637 Z= 0.336 Chirality : 0.044 0.261 2547 Planarity : 0.004 0.077 1861 Dihedral : 29.137 174.797 4411 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.83 % Allowed : 14.14 % Favored : 85.04 % 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: 1.92 (0.25), residues: 1107 helix: 2.67 (0.20), residues: 661 sheet: 0.52 (0.67), residues: 61 loop : -1.20 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 42 TYR 0.010 0.001 TYR F 51 PHE 0.047 0.002 PHE K 455 TRP 0.022 0.002 TRP K 431 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (15861) covalent geometry : angle 0.59177 / 0.34 (22634) hydrogen bonds : bond 0.05664 / 3.90 ( 864) hydrogen bonds : angle 2.80797 / 2.03 ( 2194) metal coordination : bond 0.00188 / 0.09 ( 4) metal coordination : angle 1.64529 / 0.87 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.95 seconds wall clock time: 54 minutes 14.27 seconds (3254.27 seconds total)