Starting phenix.real_space_refine on Tue Dec 31 06:27:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uv9_26809/12_2024/7uv9_26809.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uv9_26809/12_2024/7uv9_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_26809/12_2024/7uv9_26809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uv9_26809/12_2024/7uv9_26809.map" model { file = "/net/cci-nas-00/data/ceres_data/7uv9_26809/12_2024/7uv9_26809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uv9_26809/12_2024/7uv9_26809.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.18, per 1000 atoms: 0.60 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: 4.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 7.05 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: 7.33 Time building geometry restraints manager: 4.48 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: 21514 1.63 - 3.26: 1362 3.26 - 4.89: 231 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=" N ILE K 311 " pdb=" CA ILE K 311 " pdb=" C ILE K 311 " ideal model delta sigma weight residual 110.42 114.71 -4.29 9.60e-01 1.09e+00 2.00e+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: 2227 0.066 - 0.132: 275 0.132 - 0.199: 77 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: 3.280 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 41.410 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 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= 0.527 Angle : 0.890 8.149 23175 Z= 0.554 Chirality : 0.055 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.057 0.015 TRP K 247 HIS 0.021 0.004 HIS K 225 PHE 0.058 0.007 PHE K 215 TYR 0.042 0.005 TYR K 222 ARG 0.029 0.001 ARG K 339 *********************** 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 : 1.162 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: 0.3835 time to fit residues: 87.9059 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 : 1.246 ------------------------------------------------------------------------------- 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 117 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 24 GLN C 73 ASN C 104 GLN F 25 ASN K 176 HIS K 226 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16229 Z= 0.347 Angle : 0.665 5.783 23175 Z= 0.391 Chirality : 0.042 0.159 2606 Planarity : 0.006 0.047 1927 Dihedral : 29.524 179.283 4485 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.10 % Allowed : 7.32 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1138 helix: 1.65 (0.20), residues: 675 sheet: 0.88 (0.64), residues: 66 loop : -1.01 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 247 HIS 0.007 0.001 HIS K 223 PHE 0.023 0.003 PHE K 93 TYR 0.015 0.002 TYR K 330 ARG 0.006 0.001 ARG K 175 *********************** 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 154 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7900 (t0) cc_final: 0.7482 (t0) REVERT: K 140 LEU cc_start: 0.1393 (OUTLIER) cc_final: 0.1137 (mm) REVERT: K 191 MET cc_start: 0.1311 (mtt) cc_final: 0.0584 (tpt) REVERT: K 317 ARG cc_start: 0.1750 (mtm-85) cc_final: 0.1424 (mtp-110) REVERT: K 332 MET cc_start: 0.1705 (tpp) cc_final: 0.0786 (tpp) REVERT: K 466 ASP cc_start: 0.1001 (OUTLIER) cc_final: 0.0767 (p0) outliers start: 11 outliers final: 4 residues processed: 151 average time/residue: 0.4091 time to fit residues: 84.3088 Evaluate side-chains 134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain K residue 201 LEU 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 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 125 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 109 HIS K 114 ASN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 515 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16229 Z= 0.180 Angle : 0.542 9.228 23175 Z= 0.323 Chirality : 0.036 0.146 2606 Planarity : 0.004 0.047 1927 Dihedral : 29.299 177.904 4481 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.70 % Allowed : 9.63 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1138 helix: 2.20 (0.20), residues: 667 sheet: 1.12 (0.65), residues: 66 loop : -0.75 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 247 HIS 0.004 0.001 HIS K 223 PHE 0.008 0.001 PHE K 215 TYR 0.017 0.001 TYR K 222 ARG 0.004 0.000 ARG D 86 *********************** 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 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7829 (t0) cc_final: 0.7315 (t0) REVERT: D 52 THR cc_start: 0.8052 (m) cc_final: 0.7748 (m) REVERT: K 79 LYS cc_start: 0.3590 (mptt) cc_final: 0.3314 (pttm) REVERT: K 191 MET cc_start: 0.1534 (mtt) cc_final: 0.0193 (tpt) REVERT: K 317 ARG cc_start: 0.2056 (mtm-85) cc_final: 0.1506 (mtp-110) REVERT: K 466 ASP cc_start: 0.1002 (OUTLIER) cc_final: 0.0799 (p0) outliers start: 7 outliers final: 3 residues processed: 141 average time/residue: 0.3867 time to fit residues: 73.7316 Evaluate side-chains 130 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 466 ASP 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 124 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16229 Z= 0.220 Angle : 0.567 11.149 23175 Z= 0.335 Chirality : 0.037 0.153 2606 Planarity : 0.004 0.045 1927 Dihedral : 29.335 178.805 4481 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.20 % Allowed : 10.43 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1138 helix: 2.08 (0.20), residues: 672 sheet: 1.09 (0.64), residues: 66 loop : -1.02 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 221 HIS 0.004 0.001 HIS G 31 PHE 0.010 0.001 PHE K 215 TYR 0.020 0.001 TYR K 222 ARG 0.003 0.000 ARG D 86 *********************** 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 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7837 (t0) cc_final: 0.7316 (t0) REVERT: D 52 THR cc_start: 0.8081 (m) cc_final: 0.7792 (m) REVERT: K 79 LYS cc_start: 0.3654 (mptt) cc_final: 0.3235 (pttp) REVERT: K 191 MET cc_start: 0.1534 (mtt) cc_final: 0.0200 (tpt) REVERT: K 317 ARG cc_start: 0.2662 (mtm-85) cc_final: 0.1176 (ptm-80) REVERT: K 332 MET cc_start: 0.1712 (tpp) cc_final: 0.0900 (tpp) outliers start: 12 outliers final: 8 residues processed: 139 average time/residue: 0.3765 time to fit residues: 71.4349 Evaluate side-chains 132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 77 ILE Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 199 TYR 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 111 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16229 Z= 0.183 Angle : 0.541 9.839 23175 Z= 0.323 Chirality : 0.036 0.129 2606 Planarity : 0.004 0.045 1927 Dihedral : 29.280 178.719 4481 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.30 % Allowed : 11.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1138 helix: 2.30 (0.20), residues: 670 sheet: 1.12 (0.63), residues: 66 loop : -0.82 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 221 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE K 215 TYR 0.019 0.001 TYR K 222 ARG 0.002 0.000 ARG D 86 *********************** 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 140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7847 (t0) cc_final: 0.7337 (t0) REVERT: D 52 THR cc_start: 0.8080 (m) cc_final: 0.7780 (m) REVERT: F 59 LYS cc_start: 0.7884 (tttm) cc_final: 0.7625 (tttt) REVERT: K 79 LYS cc_start: 0.3745 (mptt) cc_final: 0.3305 (pttp) REVERT: K 156 MET cc_start: 0.0935 (mtm) cc_final: 0.0493 (ptp) REVERT: K 191 MET cc_start: 0.1407 (mtt) cc_final: 0.0552 (tpt) REVERT: K 317 ARG cc_start: 0.2823 (mtm-85) cc_final: 0.1272 (ptm-80) REVERT: K 332 MET cc_start: 0.1807 (tpp) cc_final: 0.0995 (tpp) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.3735 time to fit residues: 68.3117 Evaluate side-chains 137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 77 ILE 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 270 LEU Chi-restraints excluded: chain K residue 480 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.0060 chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 49 HIS ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16229 Z= 0.148 Angle : 0.506 9.068 23175 Z= 0.303 Chirality : 0.034 0.129 2606 Planarity : 0.004 0.045 1927 Dihedral : 29.129 178.159 4481 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.00 % Allowed : 12.34 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.26), residues: 1138 helix: 2.59 (0.20), residues: 670 sheet: 1.08 (0.61), residues: 64 loop : -0.68 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 247 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE K 215 TYR 0.017 0.001 TYR K 222 ARG 0.002 0.000 ARG D 86 *********************** 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 141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7741 (t0) cc_final: 0.7236 (t0) REVERT: D 52 THR cc_start: 0.7999 (m) cc_final: 0.7676 (m) REVERT: F 59 LYS cc_start: 0.7863 (tttm) cc_final: 0.7594 (tmtt) REVERT: K 79 LYS cc_start: 0.3489 (mptt) cc_final: 0.3262 (pttp) REVERT: K 156 MET cc_start: 0.0848 (mtm) cc_final: 0.0495 (ptp) REVERT: K 191 MET cc_start: 0.1510 (mtt) cc_final: 0.0745 (tpt) REVERT: K 317 ARG cc_start: 0.3032 (mtm-85) cc_final: 0.1221 (ptm-80) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.3671 time to fit residues: 68.3143 Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 270 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 109 HIS K 239 HIS ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 16229 Z= 0.507 Angle : 0.763 9.455 23175 Z= 0.436 Chirality : 0.048 0.169 2606 Planarity : 0.006 0.057 1927 Dihedral : 29.722 177.694 4481 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.50 % Allowed : 12.64 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1138 helix: 1.51 (0.20), residues: 683 sheet: 0.63 (0.61), residues: 65 loop : -1.18 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP K 516 HIS 0.010 0.002 HIS G 31 PHE 0.024 0.003 PHE K 257 TYR 0.026 0.003 TYR K 330 ARG 0.007 0.001 ARG E 116 *********************** 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 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.212 Fit side-chains REVERT: C 73 ASN cc_start: 0.7990 (t0) cc_final: 0.7566 (t0) REVERT: K 14 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6207 (tt) REVERT: K 93 PHE cc_start: 0.1977 (OUTLIER) cc_final: 0.0852 (m-80) REVERT: K 191 MET cc_start: 0.1618 (mtt) cc_final: 0.0465 (tpt) REVERT: K 202 MET cc_start: 0.3614 (mmt) cc_final: 0.3049 (ptp) REVERT: K 332 MET cc_start: 0.1657 (tpp) cc_final: 0.0965 (tpp) outliers start: 15 outliers final: 12 residues processed: 141 average time/residue: 0.3622 time to fit residues: 70.1228 Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 220 VAL 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 53 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 105 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16229 Z= 0.213 Angle : 0.577 8.756 23175 Z= 0.342 Chirality : 0.037 0.141 2606 Planarity : 0.004 0.044 1927 Dihedral : 29.404 179.219 4481 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1138 helix: 2.06 (0.20), residues: 669 sheet: 0.48 (0.62), residues: 66 loop : -1.04 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP K 334 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE K 257 TYR 0.017 0.001 TYR K 130 ARG 0.003 0.000 ARG K 339 *********************** 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 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.243 Fit side-chains REVERT: C 73 ASN cc_start: 0.7959 (t0) cc_final: 0.7479 (t0) REVERT: D 52 THR cc_start: 0.8123 (m) cc_final: 0.7828 (m) REVERT: F 59 LYS cc_start: 0.7929 (tttm) cc_final: 0.7690 (tttt) REVERT: K 14 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6102 (tt) REVERT: K 191 MET cc_start: 0.1676 (mtt) cc_final: 0.0771 (tpt) REVERT: K 202 MET cc_start: 0.3350 (mmt) cc_final: 0.2450 (mtp) outliers start: 10 outliers final: 8 residues processed: 137 average time/residue: 0.3780 time to fit residues: 70.0296 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 : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 119 ILE 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 128 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 158 GLN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16229 Z= 0.305 Angle : 0.639 8.694 23175 Z= 0.372 Chirality : 0.040 0.141 2606 Planarity : 0.005 0.043 1927 Dihedral : 29.526 179.915 4481 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.30 % Allowed : 12.74 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1138 helix: 1.75 (0.20), residues: 674 sheet: 0.36 (0.63), residues: 66 loop : -1.31 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 334 HIS 0.006 0.001 HIS G 31 PHE 0.026 0.002 PHE K 324 TYR 0.018 0.002 TYR K 330 ARG 0.004 0.000 ARG E 116 *********************** 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 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.331 Fit side-chains REVERT: C 73 ASN cc_start: 0.7975 (t0) cc_final: 0.7511 (t0) REVERT: K 14 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6120 (tt) REVERT: K 191 MET cc_start: 0.1776 (mtt) cc_final: 0.0939 (tpt) REVERT: K 202 MET cc_start: 0.3609 (mmt) cc_final: 0.2596 (mtp) outliers start: 13 outliers final: 11 residues processed: 136 average time/residue: 0.3909 time to fit residues: 72.6285 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 : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 220 VAL 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 80 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 171 ASN ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16229 Z= 0.359 Angle : 0.686 9.989 23175 Z= 0.396 Chirality : 0.043 0.151 2606 Planarity : 0.005 0.046 1927 Dihedral : 29.679 179.417 4481 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.20 % Allowed : 12.94 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1138 helix: 1.49 (0.20), residues: 681 sheet: -0.05 (0.62), residues: 65 loop : -1.37 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 334 HIS 0.007 0.002 HIS G 31 PHE 0.024 0.002 PHE K 257 TYR 0.019 0.002 TYR K 330 ARG 0.005 0.001 ARG K 267 ********************** 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 141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.272 Fit side-chains REVERT: C 73 ASN cc_start: 0.8001 (t0) cc_final: 0.7566 (t0) REVERT: F 59 LYS cc_start: 0.8011 (tttm) cc_final: 0.7626 (tttt) REVERT: K 14 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6137 (tt) REVERT: K 191 MET cc_start: 0.1602 (mtt) cc_final: 0.0851 (tpt) REVERT: K 202 MET cc_start: 0.3771 (mmt) cc_final: 0.2574 (mtp) outliers start: 12 outliers final: 10 residues processed: 139 average time/residue: 0.3791 time to fit residues: 71.4915 Evaluate side-chains 135 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 220 VAL 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 33 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4239 r_free = 0.4239 target = 0.174882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133865 restraints weight = 26107.854| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.85 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16229 Z= 0.190 Angle : 0.571 10.654 23175 Z= 0.336 Chirality : 0.036 0.140 2606 Planarity : 0.004 0.046 1927 Dihedral : 29.372 178.705 4481 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.10 % Allowed : 13.84 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1138 helix: 2.12 (0.20), residues: 669 sheet: 0.28 (0.64), residues: 66 loop : -1.08 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 334 HIS 0.004 0.001 HIS B 75 PHE 0.019 0.001 PHE K 324 TYR 0.016 0.001 TYR K 222 ARG 0.002 0.000 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.43 seconds wall clock time: 46 minutes 36.00 seconds (2796.00 seconds total)