Starting phenix.real_space_refine on Sat Sep 12 09:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uv9_26809/09_2026/7uv9_26809.map" } resolution = 3.2 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= 0.002 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 Fe 1 7.16 5 P 292 5.49 5 S 33 5.16 5 C 8766 2.51 5 N 2815 2.21 5 O 3435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 15342 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3014 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2972 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 407, 3379 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 19, 'TRANS': 387} Chain breaks: 3 Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'OH0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15342 At special positions: 0 Unit cell: (91, 158.34, 152.88, 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) Fe 1 26.01 S 33 16.00 P 292 15.00 O 3435 8.00 N 2815 7.00 C 8766 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: 1.29 Conformation dependent library (CDL) restraints added in 588.6 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 62.4% alpha, 6.6% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.553A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.649A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.570A 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 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.044A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.755A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (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: 3.501A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.569A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.736A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.817A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.781A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.587A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.866A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.715A 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: 3.604A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.515A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.602A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.644A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.501A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.766A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 46 Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 123 through 132 Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 153 through 157 Processing helix chain 'K' and resid 160 through 167 removed outlier: 3.721A pdb=" N ASP K 164 " --> pdb=" O PRO K 160 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE K 165 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 166 " --> pdb=" O THR K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 173 removed outlier: 3.583A pdb=" N TRP K 173 " --> pdb=" O VAL K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 179 Processing helix chain 'K' and resid 187 through 191 Processing helix chain 'K' and resid 214 through 218 Processing helix chain 'K' and resid 237 through 251 removed outlier: 3.539A pdb=" N GLY K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 262 removed outlier: 3.789A pdb=" N ARG K 261 " --> pdb=" O PHE K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 318 Processing helix chain 'K' and resid 321 through 325 Processing helix chain 'K' and resid 328 through 346 Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 454 through 470 Processing helix chain 'K' and resid 472 through 477 removed outlier: 4.420A pdb=" N CYS K 477 " --> pdb=" O LEU K 473 " (cutoff:3.500A) Processing helix chain 'K' and resid 484 through 500 Processing helix chain 'K' and resid 503 through 508 removed outlier: 3.835A pdb=" N LEU K 508 " --> pdb=" O PRO K 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.157A 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: 3.547A 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: 7.460A 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: 6.992A 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: 6.910A 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: 3.574A 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: 7.072A 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 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 55 through 56 removed outlier: 6.388A pdb=" N THR K 55 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU K 293 " --> pdb=" O HIS K 225 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS K 200 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER K 145 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE K 144 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ASP K 109 " --> pdb=" O ILE K 144 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU K 146 " --> pdb=" O MET K 107 " (cutoff:3.500A) removed outlier: 11.009A pdb=" N MET K 107 " --> pdb=" O LEU K 146 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS K 117 " --> pdb=" O ASP K 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 208 through 212 removed outlier: 4.058A pdb=" N PHE K 211 " --> pdb=" O HIS K 284 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS K 284 " --> pdb=" O PHE K 211 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1794 1.30 - 1.44: 5928 1.44 - 1.58: 7861 1.58 - 1.72: 589 1.72 - 1.86: 57 Bond restraints: 16229 Sorted by residual: bond pdb=" C LYS K 79 " pdb=" O LYS K 79 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.26e-02 6.30e+03 3.86e+01 bond pdb=" CA SER K 161 " pdb=" C SER K 161 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.32e-02 5.74e+03 2.64e+01 bond pdb=" CA LEU K 464 " pdb=" C LEU K 464 " ideal model delta sigma weight residual 1.524 1.588 -0.065 1.27e-02 6.20e+03 2.59e+01 bond pdb=" C ILE K 305 " pdb=" O ILE K 305 " ideal model delta sigma weight residual 1.242 1.199 0.043 8.60e-03 1.35e+04 2.51e+01 bond pdb=" CA TYR K 49 " pdb=" C TYR K 49 " ideal model delta sigma weight residual 1.526 1.480 0.046 9.70e-03 1.06e+04 2.27e+01 ... (remaining 16224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 20924 1.63 - 3.26: 1934 3.26 - 4.89: 249 4.89 - 6.52: 53 6.52 - 8.15: 15 Bond angle restraints: 23175 Sorted by residual: angle pdb=" N THR K 237 " pdb=" CA THR K 237 " pdb=" C THR K 237 " ideal model delta sigma weight residual 110.53 103.44 7.09 1.32e+00 5.74e-01 2.89e+01 angle pdb=" N GLY K 481 " pdb=" CA GLY K 481 " pdb=" C GLY K 481 " ideal model delta sigma weight residual 114.67 120.35 -5.68 1.10e+00 8.26e-01 2.67e+01 angle pdb=" N ASP K 491 " pdb=" CA ASP K 491 " pdb=" C ASP K 491 " ideal model delta sigma weight residual 111.36 116.61 -5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N LEU K 359 " pdb=" CA LEU K 359 " pdb=" C LEU K 359 " ideal model delta sigma weight residual 111.33 117.03 -5.70 1.21e+00 6.83e-01 2.22e+01 angle pdb=" O4' DC J -62 " pdb=" C1' DC J -62 " pdb=" N1 DC J -62 " ideal model delta sigma weight residual 108.00 111.14 -3.14 7.00e-01 2.04e+00 2.01e+01 ... (remaining 23170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 7495 35.26 - 70.53: 1455 70.53 - 105.79: 25 105.79 - 141.05: 0 141.05 - 176.32: 1 Dihedral angle restraints: 8976 sinusoidal: 5597 harmonic: 3379 Sorted by residual: 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 43.68 176.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA THR K 218 " pdb=" C THR K 218 " pdb=" N SER K 219 " pdb=" CA SER K 219 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" C PHE K 215 " pdb=" N PHE K 215 " pdb=" CA PHE K 215 " pdb=" CB PHE K 215 " ideal model delta harmonic sigma weight residual -122.60 -131.37 8.77 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2104 0.066 - 0.132: 397 0.132 - 0.199: 78 0.199 - 0.265: 19 0.265 - 0.331: 8 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CA PHE K 215 " pdb=" N PHE K 215 " pdb=" C PHE K 215 " pdb=" CB PHE K 215 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA THR K 209 " pdb=" N THR K 209 " pdb=" C THR K 209 " pdb=" CB THR K 209 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA TYR K 222 " pdb=" N TYR K 222 " pdb=" C TYR K 222 " pdb=" CB TYR K 222 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2603 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N OH0 K 701 " 0.034 2.00e-02 2.50e+03 1.18e-01 2.09e+02 pdb=" O OH0 K 701 " -0.164 2.00e-02 2.50e+03 pdb=" C5 OH0 K 701 " -0.156 2.00e-02 2.50e+03 pdb=" C6 OH0 K 701 " 0.045 2.00e-02 2.50e+03 pdb=" C7 OH0 K 701 " 0.112 2.00e-02 2.50e+03 pdb=" O3 OH0 K 701 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 221 " 0.055 2.00e-02 2.50e+03 2.67e-02 1.79e+01 pdb=" CG TRP K 221 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP K 221 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP K 221 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP K 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 221 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP K 221 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 221 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 221 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP K 221 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 247 " 0.049 2.00e-02 2.50e+03 2.65e-02 1.75e+01 pdb=" CG TRP K 247 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP K 247 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP K 247 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP K 247 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP K 247 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP K 247 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 247 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 247 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 247 " 0.018 2.00e-02 2.50e+03 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 6 2.23 - 2.90: 5058 2.90 - 3.56: 21208 3.56 - 4.23: 39510 4.23 - 4.90: 60663 Nonbonded interactions: 126445 Sorted by model distance: nonbonded pdb=" OE1 GLU K 41 " pdb=" NE2 HIS K 45 " model vdw 1.561 3.120 nonbonded pdb=" O OH0 K 701 " pdb="FE FE K 702 " model vdw 2.037 2.260 nonbonded pdb=" OD1 ASP K 214 " pdb="FE FE K 702 " model vdw 2.159 2.260 nonbonded pdb=" O3 OH0 K 701 " pdb="FE FE K 702 " model vdw 2.203 2.260 nonbonded pdb=" NE2 HIS K 212 " pdb="FE FE K 702 " model vdw 2.208 2.340 ... (remaining 126440 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 43 through 134) selection = (chain 'E' and resid 43 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 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=0.58 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: 3.150 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.009 0.093 16229 Z= 0.698 Angle : 0.988 8.149 23175 Z= 0.758 Chirality : 0.060 0.331 2606 Planarity : 0.007 0.118 1927 Dihedral : 26.048 176.319 6798 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.30 % Allowed : 2.41 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1138 helix: 1.94 (0.21), residues: 645 sheet: 0.84 (0.64), residues: 63 loop : -0.99 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG K 339 TYR 0.042 0.005 TYR K 222 PHE 0.058 0.007 PHE K 215 TRP 0.057 0.015 TRP K 247 HIS 0.021 0.004 HIS K 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.70 (16229) covalent geometry : angle 0.98770 / 0.76 (23175) hydrogen bonds : bond 0.11749 / 7.95 ( 886) hydrogen bonds : angle 4.01512 / 2.99 ( 2222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7756 (t0) cc_final: 0.7396 (t0) REVERT: D 31 ARG cc_start: 0.4458 (OUTLIER) cc_final: 0.3048 (ttm110) REVERT: K 120 GLU cc_start: 0.4573 (mt-10) cc_final: 0.4121 (mt-10) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.1576 time to fit residues: 36.4944 Evaluate side-chains 138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN F 25 ASN H 49 HIS H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.176945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135750 restraints weight = 26517.951| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.90 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 16229 Z= 0.169 Angle : 0.626 6.976 23175 Z= 0.372 Chirality : 0.046 0.260 2606 Planarity : 0.005 0.059 1927 Dihedral : 29.259 177.655 4485 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.80 % Allowed : 6.02 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.25), residues: 1138 helix: 2.08 (0.20), residues: 666 sheet: 0.80 (0.63), residues: 66 loop : -0.74 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 339 TYR 0.012 0.002 TYR H 42 PHE 0.031 0.002 PHE K 93 TRP 0.028 0.003 TRP K 247 HIS 0.008 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (16229) covalent geometry : angle 0.62594 / 0.37 (23175) hydrogen bonds : bond 0.06571 / 4.34 ( 886) hydrogen bonds : angle 3.40670 / 2.51 ( 2222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.418 Fit side-chains REVERT: C 73 ASN cc_start: 0.7865 (t0) cc_final: 0.7267 (t0) REVERT: K 191 MET cc_start: 0.1504 (mtt) cc_final: -0.0221 (tpt) REVERT: K 269 GLU cc_start: 0.2650 (OUTLIER) cc_final: 0.2437 (tt0) REVERT: K 332 MET cc_start: 0.1673 (tpp) cc_final: 0.0961 (tpp) outliers start: 8 outliers final: 2 residues processed: 147 average time/residue: 0.1492 time to fit residues: 30.0775 Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 269 GLU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 20 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 138 optimal weight: 50.0000 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 104 GLN K 176 HIS ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136830 restraints weight = 26556.721| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.91 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16229 Z= 0.140 Angle : 0.593 9.947 23175 Z= 0.349 Chirality : 0.045 0.291 2606 Planarity : 0.004 0.056 1927 Dihedral : 29.385 178.090 4481 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.60 % Allowed : 7.92 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1138 helix: 2.26 (0.20), residues: 669 sheet: 0.97 (0.63), residues: 64 loop : -0.73 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.021 0.001 TYR K 222 PHE 0.014 0.001 PHE K 93 TRP 0.020 0.002 TRP K 247 HIS 0.005 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (16229) covalent geometry : angle 0.59318 / 0.35 (23175) hydrogen bonds : bond 0.05982 / 3.95 ( 886) hydrogen bonds : angle 3.25916 / 2.40 ( 2222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7931 (t0) cc_final: 0.7289 (t0) REVERT: D 31 ARG cc_start: 0.3422 (ttm110) cc_final: 0.3063 (tpt-90) REVERT: K 172 MET cc_start: -0.1672 (mtm) cc_final: -0.1959 (mmm) REVERT: K 191 MET cc_start: 0.1714 (mtt) cc_final: 0.0340 (tpt) REVERT: K 332 MET cc_start: 0.1749 (tpp) cc_final: 0.0681 (tpp) outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 0.1580 time to fit residues: 28.9475 Evaluate side-chains 125 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN F 25 ASN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136607 restraints weight = 26632.691| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.92 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16229 Z= 0.135 Angle : 0.576 7.520 23175 Z= 0.338 Chirality : 0.044 0.323 2606 Planarity : 0.004 0.053 1927 Dihedral : 29.463 178.171 4481 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.00 % Allowed : 8.83 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1138 helix: 2.40 (0.20), residues: 668 sheet: 1.06 (0.65), residues: 64 loop : -0.74 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.027 0.001 TYR K 222 PHE 0.011 0.001 PHE K 295 TRP 0.017 0.002 TRP K 247 HIS 0.003 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (16229) covalent geometry : angle 0.57590 / 0.34 (23175) hydrogen bonds : bond 0.05831 / 3.86 ( 886) hydrogen bonds : angle 3.16153 / 2.32 ( 2222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.315 Fit side-chains REVERT: C 73 ASN cc_start: 0.7906 (t0) cc_final: 0.7310 (t0) REVERT: D 31 ARG cc_start: 0.3561 (ttm110) cc_final: 0.3084 (tpt-90) REVERT: D 52 THR cc_start: 0.8258 (m) cc_final: 0.7955 (m) REVERT: K 172 MET cc_start: -0.1580 (mtm) cc_final: -0.2050 (mmm) REVERT: K 191 MET cc_start: 0.1510 (mtt) cc_final: -0.0070 (tpt) REVERT: K 332 MET cc_start: 0.1659 (tpp) cc_final: 0.0780 (tpp) outliers start: 10 outliers final: 5 residues processed: 138 average time/residue: 0.1506 time to fit residues: 28.5344 Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 114 ASN K 226 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 515 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.175092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134164 restraints weight = 26559.180| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.90 r_work: 0.3062 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16229 Z= 0.166 Angle : 0.621 7.327 23175 Z= 0.358 Chirality : 0.046 0.263 2606 Planarity : 0.004 0.051 1927 Dihedral : 29.579 178.803 4481 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.00 % Allowed : 10.73 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1138 helix: 2.23 (0.20), residues: 666 sheet: 1.04 (0.65), residues: 64 loop : -1.00 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 AARG K 152 TYR 0.013 0.002 TYR K 312 PHE 0.012 0.002 PHE K 215 TRP 0.013 0.002 TRP K 247 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (16229) covalent geometry : angle 0.62092 / 0.36 (23175) hydrogen bonds : bond 0.07005 / 4.65 ( 886) hydrogen bonds : angle 3.25049 / 2.38 ( 2222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.421 Fit side-chains REVERT: C 73 ASN cc_start: 0.8137 (t0) cc_final: 0.7453 (t0) REVERT: K 156 MET cc_start: 0.1283 (mtm) cc_final: 0.0763 (ptp) REVERT: K 172 MET cc_start: 0.0737 (mtm) cc_final: -0.0745 (mmm) REVERT: K 191 MET cc_start: -0.0019 (mtt) cc_final: -0.0672 (tpt) REVERT: K 193 TYR cc_start: 0.0521 (p90) cc_final: 0.0223 (p90) REVERT: K 317 ARG cc_start: 0.1633 (mtm-85) cc_final: 0.1049 (mtp-110) outliers start: 10 outliers final: 9 residues processed: 137 average time/residue: 0.1542 time to fit residues: 29.1999 Evaluate side-chains 133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 480 THR Chi-restraints excluded: chain K residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.0670 chunk 132 optimal weight: 0.0010 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 25 ASN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133779 restraints weight = 26404.945| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.92 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16229 Z= 0.142 Angle : 0.594 7.338 23175 Z= 0.344 Chirality : 0.045 0.267 2606 Planarity : 0.004 0.050 1927 Dihedral : 29.589 179.009 4481 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.20 % Allowed : 10.53 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1138 helix: 2.38 (0.20), residues: 669 sheet: 0.88 (0.63), residues: 64 loop : -0.83 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.029 0.001 TYR K 222 PHE 0.009 0.001 PHE K 215 TRP 0.012 0.002 TRP K 247 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (16229) covalent geometry : angle 0.59449 / 0.34 (23175) hydrogen bonds : bond 0.06361 / 4.21 ( 886) hydrogen bonds : angle 3.16938 / 2.32 ( 2222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.430 Fit side-chains REVERT: C 73 ASN cc_start: 0.7977 (t0) cc_final: 0.7372 (t0) REVERT: D 52 THR cc_start: 0.8202 (m) cc_final: 0.7888 (m) REVERT: K 156 MET cc_start: 0.0990 (mtm) cc_final: 0.0391 (ptp) REVERT: K 172 MET cc_start: -0.1610 (mtm) cc_final: -0.2155 (mmm) REVERT: K 191 MET cc_start: 0.1489 (mtt) cc_final: -0.0024 (tpt) REVERT: K 193 TYR cc_start: 0.0050 (p90) cc_final: -0.0296 (p90) REVERT: K 270 LEU cc_start: 0.0859 (OUTLIER) cc_final: 0.0136 (mm) REVERT: K 317 ARG cc_start: 0.1735 (mtm-85) cc_final: 0.1481 (mtp-110) outliers start: 12 outliers final: 8 residues processed: 132 average time/residue: 0.1665 time to fit residues: 30.1369 Evaluate side-chains 135 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.176823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136188 restraints weight = 26329.745| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.70 r_work: 0.3146 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16229 Z= 0.129 Angle : 0.579 8.302 23175 Z= 0.336 Chirality : 0.044 0.268 2606 Planarity : 0.004 0.050 1927 Dihedral : 29.579 178.818 4481 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.00 % Allowed : 11.43 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.26), residues: 1138 helix: 2.53 (0.20), residues: 669 sheet: 0.85 (0.65), residues: 64 loop : -0.75 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 106 TYR 0.016 0.001 TYR K 130 PHE 0.011 0.001 PHE K 295 TRP 0.012 0.002 TRP K 247 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (16229) covalent geometry : angle 0.57862 / 0.34 (23175) hydrogen bonds : bond 0.05727 / 3.77 ( 886) hydrogen bonds : angle 3.09064 / 2.25 ( 2222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.449 Fit side-chains REVERT: C 73 ASN cc_start: 0.8154 (t0) cc_final: 0.7480 (t0) REVERT: D 52 THR cc_start: 0.8350 (m) cc_final: 0.8052 (m) REVERT: K 156 MET cc_start: 0.1348 (mtm) cc_final: 0.0738 (ptp) REVERT: K 172 MET cc_start: 0.0217 (mtm) cc_final: -0.0606 (mmm) REVERT: K 191 MET cc_start: 0.0109 (mtt) cc_final: -0.0683 (tpt) REVERT: K 317 ARG cc_start: 0.1677 (mtm-85) cc_final: 0.1092 (mtp-110) outliers start: 10 outliers final: 9 residues processed: 131 average time/residue: 0.1692 time to fit residues: 30.0976 Evaluate side-chains 133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.176411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135180 restraints weight = 26612.101| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.74 r_work: 0.3115 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16229 Z= 0.135 Angle : 0.577 9.690 23175 Z= 0.333 Chirality : 0.044 0.267 2606 Planarity : 0.004 0.049 1927 Dihedral : 29.588 178.830 4481 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.20 % Allowed : 11.74 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.26), residues: 1138 helix: 2.52 (0.20), residues: 670 sheet: 0.77 (0.64), residues: 64 loop : -0.78 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 33 TYR 0.025 0.001 TYR K 222 PHE 0.012 0.001 PHE K 62 TRP 0.020 0.002 TRP K 126 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (16229) covalent geometry : angle 0.57653 / 0.33 (23175) hydrogen bonds : bond 0.05866 / 3.87 ( 886) hydrogen bonds : angle 3.10936 / 2.28 ( 2222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8147 (t0) cc_final: 0.7478 (t0) REVERT: D 52 THR cc_start: 0.8406 (m) cc_final: 0.8107 (m) REVERT: K 79 LYS cc_start: 0.5300 (pttm) cc_final: 0.5066 (pttp) REVERT: K 156 MET cc_start: 0.1360 (mtm) cc_final: 0.0722 (ptp) REVERT: K 191 MET cc_start: 0.0143 (mtt) cc_final: -0.0689 (tpt) REVERT: K 317 ARG cc_start: 0.2086 (mtm-85) cc_final: 0.1230 (mtp-110) outliers start: 12 outliers final: 11 residues processed: 138 average time/residue: 0.1700 time to fit residues: 32.3113 Evaluate side-chains 136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 199 TYR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 28 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134178 restraints weight = 26347.257| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.73 r_work: 0.3078 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16229 Z= 0.178 Angle : 0.640 8.901 23175 Z= 0.363 Chirality : 0.047 0.261 2606 Planarity : 0.005 0.049 1927 Dihedral : 29.634 179.778 4481 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.20 % Allowed : 12.24 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1138 helix: 2.14 (0.20), residues: 678 sheet: 0.67 (0.64), residues: 64 loop : -1.00 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.039 0.002 TYR K 130 PHE 0.014 0.002 PHE K 215 TRP 0.017 0.003 TRP K 126 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (16229) covalent geometry : angle 0.63966 / 0.36 (23175) hydrogen bonds : bond 0.07348 / 4.87 ( 886) hydrogen bonds : angle 3.27231 / 2.40 ( 2222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8209 (t0) cc_final: 0.7548 (t0) REVERT: K 191 MET cc_start: 0.0002 (mtt) cc_final: -0.0682 (tpt) REVERT: K 222 TYR cc_start: 0.1865 (t80) cc_final: 0.1563 (m-80) REVERT: K 317 ARG cc_start: 0.2497 (mtm-85) cc_final: 0.1233 (ptm-80) outliers start: 12 outliers final: 11 residues processed: 131 average time/residue: 0.1691 time to fit residues: 30.4374 Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 199 TYR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 121 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138557 restraints weight = 26601.609| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.69 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16229 Z= 0.132 Angle : 0.597 14.409 23175 Z= 0.341 Chirality : 0.044 0.270 2606 Planarity : 0.004 0.050 1927 Dihedral : 29.605 179.585 4481 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.00 % Allowed : 11.84 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.26), residues: 1138 helix: 2.45 (0.20), residues: 670 sheet: 0.72 (0.65), residues: 64 loop : -0.80 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 339 TYR 0.014 0.001 TYR K 193 PHE 0.007 0.001 PHE K 215 TRP 0.017 0.002 TRP K 126 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (16229) covalent geometry : angle 0.59738 / 0.34 (23175) hydrogen bonds : bond 0.05847 / 3.86 ( 886) hydrogen bonds : angle 3.13107 / 2.30 ( 2222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7955 (t0) cc_final: 0.7392 (t0) REVERT: D 52 THR cc_start: 0.8244 (m) cc_final: 0.7921 (m) REVERT: F 59 LYS cc_start: 0.7959 (tttm) cc_final: 0.7629 (tmtt) REVERT: K 191 MET cc_start: 0.1598 (mtt) cc_final: 0.0406 (tpt) REVERT: K 317 ARG cc_start: 0.2911 (mtm-85) cc_final: 0.1230 (ptm-80) outliers start: 10 outliers final: 9 residues processed: 136 average time/residue: 0.1698 time to fit residues: 31.7634 Evaluate side-chains 136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 199 TYR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.175881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134562 restraints weight = 26275.459| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.79 r_work: 0.3095 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16229 Z= 0.138 Angle : 0.590 12.476 23175 Z= 0.338 Chirality : 0.044 0.265 2606 Planarity : 0.004 0.049 1927 Dihedral : 29.593 179.427 4481 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.90 % Allowed : 12.34 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1138 helix: 2.47 (0.20), residues: 670 sheet: 0.68 (0.65), residues: 64 loop : -0.79 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 TYR 0.026 0.001 TYR K 222 PHE 0.009 0.001 PHE K 215 TRP 0.015 0.002 TRP K 126 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (16229) covalent geometry : angle 0.59010 / 0.34 (23175) hydrogen bonds : bond 0.06010 / 3.97 ( 886) hydrogen bonds : angle 3.13589 / 2.31 ( 2222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3216.37 seconds wall clock time: 55 minutes 51.44 seconds (3351.44 seconds total)