Starting phenix.real_space_refine on Fri Jul 3 16:13:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uv9_26809/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.map" model { file = "/net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uv9_26809/07_2026/7uv9_26809.cif" } 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-dev-6108/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: 3.02, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 528.2 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: 2.25 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: 3.63 Time building geometry restraints manager: 1.63 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: 20946 1.63 - 3.26: 1913 3.26 - 4.89: 248 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: 2.340 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- 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 : 0.983 8.149 23175 Z= 0.754 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 0.98332 / 0.75 (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 : 0.461 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: 0.4120 (mt-10) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.1681 time to fit residues: 38.7324 Evaluate side-chains 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 4.9990 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: 10.0000 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 = 0.4261 r_free = 0.4261 target = 0.176826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135883 restraints weight = 26497.055| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.00 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 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 = 0.3727 r_free = 0.3727 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: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 16229 Z= 0.167 Angle : 0.619 6.718 23175 Z= 0.369 Chirality : 0.046 0.244 2606 Planarity : 0.005 0.060 1927 Dihedral : 29.319 178.269 4485 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.80 % Allowed : 6.12 % Favored : 93.08 % 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: 1.49 (0.25), residues: 1138 helix: 2.04 (0.20), residues: 668 sheet: 0.76 (0.63), residues: 66 loop : -0.78 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 339 TYR 0.012 0.001 TYR H 42 PHE 0.033 0.002 PHE K 93 TRP 0.027 0.003 TRP K 247 HIS 0.010 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (16229) covalent geometry : angle 0.61921 / 0.37 (23175) hydrogen bonds : bond 0.06573 / 4.35 ( 886) hydrogen bonds : angle 3.40571 / 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 151 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.523 Fit side-chains REVERT: C 73 ASN cc_start: 0.7867 (t0) cc_final: 0.7252 (t0) REVERT: K 191 MET cc_start: 0.1560 (mtt) cc_final: -0.0178 (tpt) REVERT: K 332 MET cc_start: 0.1767 (tpp) cc_final: 0.1088 (tpp) REVERT: K 466 ASP cc_start: 0.1252 (OUTLIER) cc_final: 0.0713 (p0) outliers start: 8 outliers final: 2 residues processed: 149 average time/residue: 0.1733 time to fit residues: 35.4671 Evaluate side-chains 132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 466 ASP 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: 0.9980 chunk 124 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 138 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.177240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135049 restraints weight = 26604.133| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.93 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16229 Z= 0.137 Angle : 0.580 10.099 23175 Z= 0.343 Chirality : 0.044 0.283 2606 Planarity : 0.004 0.056 1927 Dihedral : 29.449 178.879 4481 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.70 % Allowed : 8.32 % Favored : 90.97 % 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: 1.77 (0.25), residues: 1138 helix: 2.29 (0.20), residues: 669 sheet: 0.92 (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 0.023 0.001 TYR K 222 PHE 0.012 0.001 PHE K 93 TRP 0.019 0.002 TRP K 247 HIS 0.005 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 (16229) covalent geometry : angle 0.58015 / 0.34 (23175) hydrogen bonds : bond 0.05847 / 3.86 ( 886) hydrogen bonds : angle 3.23622 / 2.38 ( 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 140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.439 Fit side-chains REVERT: C 73 ASN cc_start: 0.7942 (t0) cc_final: 0.7280 (t0) REVERT: D 31 ARG cc_start: 0.3480 (ttm110) cc_final: 0.3076 (tpt-90) REVERT: K 172 MET cc_start: -0.1557 (mtm) cc_final: -0.1990 (mmm) REVERT: K 191 MET cc_start: 0.1676 (mtt) cc_final: 0.0278 (tpt) REVERT: K 332 MET cc_start: 0.1619 (tpp) cc_final: 0.0593 (tpp) outliers start: 7 outliers final: 3 residues processed: 137 average time/residue: 0.1680 time to fit residues: 31.7795 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 : 0.433 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 103 optimal weight: 0.0170 chunk 110 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.177667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135623 restraints weight = 26747.421| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.84 r_work: 0.3133 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16229 Z= 0.129 Angle : 0.557 7.949 23175 Z= 0.331 Chirality : 0.043 0.377 2606 Planarity : 0.004 0.052 1927 Dihedral : 29.491 178.755 4481 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.90 % Allowed : 9.03 % Favored : 90.07 % 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: 1.95 (0.25), residues: 1138 helix: 2.46 (0.20), residues: 668 sheet: 1.01 (0.65), residues: 64 loop : -0.70 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.026 0.001 TYR K 222 PHE 0.011 0.001 PHE K 257 TRP 0.017 0.002 TRP K 247 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.13 (16229) covalent geometry : angle 0.55693 / 0.33 (23175) hydrogen bonds : bond 0.05483 / 3.62 ( 886) hydrogen bonds : angle 3.14089 / 2.30 ( 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 136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.465 Fit side-chains REVERT: C 73 ASN cc_start: 0.8068 (t0) cc_final: 0.7310 (t0) REVERT: C 99 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8302 (pptt) REVERT: D 31 ARG cc_start: 0.3398 (ttm110) cc_final: 0.2979 (tpt-90) REVERT: K 172 MET cc_start: 0.0777 (mtm) cc_final: -0.0588 (mmm) REVERT: K 191 MET cc_start: 0.0041 (mtt) cc_final: -0.0760 (tpt) REVERT: K 257 PHE cc_start: 0.2923 (OUTLIER) cc_final: 0.2550 (m-80) outliers start: 9 outliers final: 4 residues processed: 133 average time/residue: 0.1691 time to fit residues: 30.8988 Evaluate side-chains 130 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 257 PHE 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: 0.5980 chunk 133 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN K 114 ASN K 226 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.175084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135356 restraints weight = 26539.911| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.87 r_work: 0.3089 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 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 = 0.3056 r_free = 0.3056 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: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16229 Z= 0.177 Angle : 0.619 7.735 23175 Z= 0.358 Chirality : 0.046 0.240 2606 Planarity : 0.005 0.050 1927 Dihedral : 29.615 179.285 4481 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.20 % Allowed : 10.03 % Favored : 88.77 % 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: 1.52 (0.25), residues: 1138 helix: 2.14 (0.20), residues: 676 sheet: 0.87 (0.65), residues: 64 loop : -1.02 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 AARG K 152 TYR 0.016 0.002 TYR K 130 PHE 0.018 0.002 PHE K 62 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 0.00352 / 0.18 (16229) covalent geometry : angle 0.61936 / 0.36 (23175) hydrogen bonds : bond 0.07083 / 4.70 ( 886) hydrogen bonds : angle 3.24511 / 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 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.309 Fit side-chains REVERT: C 73 ASN cc_start: 0.8126 (t0) cc_final: 0.7463 (t0) REVERT: K 156 MET cc_start: 0.0978 (mtm) cc_final: 0.0634 (ptp) REVERT: K 172 MET cc_start: 0.0350 (mtm) cc_final: -0.0875 (mmm) REVERT: K 191 MET cc_start: 0.0112 (mtt) cc_final: -0.0643 (tpt) REVERT: K 257 PHE cc_start: 0.2850 (OUTLIER) cc_final: 0.2496 (m-80) REVERT: K 317 ARG cc_start: 0.1603 (mtm-85) cc_final: 0.1080 (mtp-110) outliers start: 12 outliers final: 9 residues processed: 135 average time/residue: 0.1692 time to fit residues: 31.4258 Evaluate side-chains 134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 257 PHE 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: 0.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 105 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.176331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135685 restraints weight = 26454.777| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.04 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) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1796 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= 0.137 Angle : 0.578 7.292 23175 Z= 0.338 Chirality : 0.044 0.243 2606 Planarity : 0.004 0.049 1927 Dihedral : 29.622 179.558 4481 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 1.87 (0.25), residues: 1138 helix: 2.44 (0.20), residues: 668 sheet: 0.78 (0.64), residues: 64 loop : -0.78 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 95 TYR 0.025 0.001 TYR K 222 PHE 0.009 0.001 PHE K 215 TRP 0.013 0.002 TRP K 173 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (16229) covalent geometry : angle 0.57848 / 0.34 (23175) hydrogen bonds : bond 0.06183 / 4.08 ( 886) hydrogen bonds : angle 3.15029 / 2.30 ( 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: 10 poor density : 128 time to evaluate : 0.412 Fit side-chains REVERT: C 73 ASN cc_start: 0.7945 (t0) cc_final: 0.7326 (t0) REVERT: D 52 THR cc_start: 0.8274 (m) cc_final: 0.7964 (m) REVERT: K 61 ASP cc_start: 0.4484 (m-30) cc_final: 0.4195 (m-30) REVERT: K 156 MET cc_start: 0.0768 (mtm) cc_final: 0.0415 (ptp) REVERT: K 172 MET cc_start: -0.1639 (mtm) cc_final: -0.2117 (mmm) REVERT: K 191 MET cc_start: 0.1449 (mtt) cc_final: 0.0003 (tpt) REVERT: K 270 LEU cc_start: 0.0830 (OUTLIER) cc_final: 0.0018 (mm) outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 0.1591 time to fit residues: 29.3500 Evaluate side-chains 133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 308 GLN K 515 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.176675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136617 restraints weight = 26376.205| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.98 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 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 = 0.3737 r_free = 0.3737 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: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16229 Z= 0.133 Angle : 0.565 7.509 23175 Z= 0.331 Chirality : 0.043 0.247 2606 Planarity : 0.004 0.049 1927 Dihedral : 29.633 179.202 4481 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.10 % Allowed : 11.13 % Favored : 87.76 % 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: 1.97 (0.26), residues: 1138 helix: 2.53 (0.20), residues: 669 sheet: 0.71 (0.64), residues: 64 loop : -0.76 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 205 TYR 0.028 0.001 TYR K 130 PHE 0.013 0.001 PHE K 38 TRP 0.015 0.002 TRP K 126 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (16229) covalent geometry : angle 0.56547 / 0.33 (23175) hydrogen bonds : bond 0.05740 / 3.78 ( 886) hydrogen bonds : angle 3.09633 / 2.27 ( 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 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7963 (t0) cc_final: 0.7350 (t0) REVERT: D 52 THR cc_start: 0.8234 (m) cc_final: 0.7931 (m) REVERT: K 61 ASP cc_start: 0.4488 (m-30) cc_final: 0.4170 (m-30) REVERT: K 156 MET cc_start: 0.0992 (mtm) cc_final: 0.0582 (ptp) REVERT: K 172 MET cc_start: -0.1659 (mtm) cc_final: -0.2158 (mmm) REVERT: K 191 MET cc_start: 0.1518 (mtt) cc_final: 0.0128 (tpt) REVERT: K 193 TYR cc_start: -0.0135 (p90) cc_final: -0.0529 (p90) REVERT: K 202 MET cc_start: 0.0860 (ptm) cc_final: 0.0447 (tmm) outliers start: 11 outliers final: 11 residues processed: 136 average time/residue: 0.1568 time to fit residues: 29.3995 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 : 0.331 ------------------------------------------------------------------------------- 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 199 TYR Chi-restraints excluded: chain K residue 201 LEU 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: 1.9990 chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132196 restraints weight = 26265.419| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.94 r_work: 0.3024 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16229 Z= 0.219 Angle : 0.685 7.493 23175 Z= 0.388 Chirality : 0.050 0.234 2606 Planarity : 0.005 0.051 1927 Dihedral : 29.765 179.440 4481 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.20 % Allowed : 11.94 % Favored : 86.86 % 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: 1.90 (0.20), residues: 678 sheet: 0.56 (0.61), residues: 64 loop : -1.12 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 11 TYR 0.018 0.002 TYR K 330 PHE 0.051 0.003 PHE K 257 TRP 0.017 0.003 TRP K 168 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (16229) covalent geometry : angle 0.68500 / 0.39 (23175) hydrogen bonds : bond 0.08608 / 5.72 ( 886) hydrogen bonds : angle 3.42418 / 2.51 ( 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 136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8253 (t0) cc_final: 0.7573 (t0) REVERT: K 156 MET cc_start: 0.1531 (mtm) cc_final: 0.0948 (ptp) REVERT: K 191 MET cc_start: -0.0039 (mtt) cc_final: -0.0701 (tpt) REVERT: K 202 MET cc_start: 0.1715 (ptm) cc_final: 0.1040 (tmm) REVERT: K 332 MET cc_start: 0.0880 (mmm) cc_final: 0.0347 (mmt) outliers start: 12 outliers final: 10 residues processed: 134 average time/residue: 0.1684 time to fit residues: 30.9449 Evaluate side-chains 129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 199 TYR Chi-restraints excluded: chain K residue 201 LEU 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: 0.9990 chunk 105 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134499 restraints weight = 26319.404| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.78 r_work: 0.3085 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16229 Z= 0.152 Angle : 0.612 7.987 23175 Z= 0.352 Chirality : 0.046 0.247 2606 Planarity : 0.004 0.049 1927 Dihedral : 29.737 179.493 4481 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.90 % Allowed : 11.84 % Favored : 87.26 % 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: 1.53 (0.25), residues: 1138 helix: 2.19 (0.20), residues: 676 sheet: 0.67 (0.61), residues: 64 loop : -1.06 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.017 0.001 TYR K 193 PHE 0.020 0.002 PHE K 257 TRP 0.012 0.002 TRP K 221 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (16229) covalent geometry : angle 0.61196 / 0.35 (23175) hydrogen bonds : bond 0.06890 / 4.56 ( 886) hydrogen bonds : angle 3.24087 / 2.37 ( 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 133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8235 (t0) cc_final: 0.7545 (t0) REVERT: D 52 THR cc_start: 0.8442 (m) cc_final: 0.8149 (m) REVERT: K 130 TYR cc_start: 0.3833 (t80) cc_final: 0.3511 (t80) REVERT: K 156 MET cc_start: 0.1484 (mtm) cc_final: 0.0815 (ptp) REVERT: K 172 MET cc_start: 0.0490 (mtm) cc_final: -0.0544 (mmm) REVERT: K 191 MET cc_start: 0.0016 (mtt) cc_final: -0.0840 (tpt) REVERT: K 202 MET cc_start: 0.1663 (ptm) cc_final: 0.1018 (tmm) REVERT: K 332 MET cc_start: 0.0888 (mmm) cc_final: 0.0303 (mmt) outliers start: 9 outliers final: 8 residues processed: 130 average time/residue: 0.1741 time to fit residues: 30.9773 Evaluate side-chains 129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 199 TYR 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: 9.9990 chunk 12 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.175030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132669 restraints weight = 26511.744| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.73 r_work: 0.3080 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 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: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16229 Z= 0.147 Angle : 0.593 7.701 23175 Z= 0.343 Chirality : 0.044 0.246 2606 Planarity : 0.004 0.048 1927 Dihedral : 29.701 179.884 4481 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.80 % Allowed : 11.84 % Favored : 87.36 % 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: 1.70 (0.25), residues: 1138 helix: 2.30 (0.20), residues: 670 sheet: 0.78 (0.63), residues: 64 loop : -0.90 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 175 TYR 0.029 0.001 TYR K 222 PHE 0.015 0.001 PHE K 257 TRP 0.013 0.002 TRP K 221 HIS 0.005 0.001 HIS K 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (16229) covalent geometry : angle 0.59300 / 0.34 (23175) hydrogen bonds : bond 0.06462 / 4.27 ( 886) hydrogen bonds : angle 3.17868 / 2.33 ( 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 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8210 (t0) cc_final: 0.7527 (t0) REVERT: D 52 THR cc_start: 0.8429 (m) cc_final: 0.8134 (m) REVERT: K 130 TYR cc_start: 0.3885 (t80) cc_final: 0.3574 (t80) REVERT: K 156 MET cc_start: 0.1556 (mtm) cc_final: 0.0932 (ptp) REVERT: K 172 MET cc_start: 0.0528 (mtm) cc_final: -0.0543 (mmm) REVERT: K 191 MET cc_start: 0.0043 (mtt) cc_final: -0.0606 (tpt) REVERT: K 202 MET cc_start: 0.1635 (ptm) cc_final: 0.1015 (tmm) REVERT: K 332 MET cc_start: 0.0660 (mmm) cc_final: 0.0134 (mmt) outliers start: 8 outliers final: 8 residues processed: 128 average time/residue: 0.1768 time to fit residues: 30.8444 Evaluate side-chains 130 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 199 TYR 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: 6.9990 chunk 110 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 138 optimal weight: 0.0070 chunk 127 optimal weight: 0.0970 chunk 119 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.175723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133727 restraints weight = 26256.513| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.64 r_work: 0.3105 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2241 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= 0.132 Angle : 0.587 9.300 23175 Z= 0.339 Chirality : 0.045 0.488 2606 Planarity : 0.004 0.047 1927 Dihedral : 29.689 179.892 4481 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.90 % Allowed : 11.94 % 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: 1.84 (0.26), residues: 1138 helix: 2.42 (0.20), residues: 670 sheet: 0.76 (0.63), residues: 64 loop : -0.83 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 339 TYR 0.015 0.001 TYR K 193 PHE 0.017 0.001 PHE K 257 TRP 0.012 0.002 TRP K 221 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.13 (16229) covalent geometry : angle 0.58699 / 0.34 (23175) hydrogen bonds : bond 0.05956 / 3.93 ( 886) hydrogen bonds : angle 3.14993 / 2.30 ( 2222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3441.44 seconds wall clock time: 59 minutes 45.28 seconds (3585.28 seconds total)