Starting phenix.real_space_refine on Tue Nov 18 15:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e0p_8949/11_2025/6e0p_8949.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e0p_8949/11_2025/6e0p_8949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e0p_8949/11_2025/6e0p_8949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e0p_8949/11_2025/6e0p_8949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e0p_8949/11_2025/6e0p_8949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e0p_8949/11_2025/6e0p_8949.map" } resolution = 2.6 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= 0.004 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 26 5.16 5 C 8921 2.51 5 N 2815 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15567 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1789 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "N" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1787 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Time building chain proxies: 3.73, per 1000 atoms: 0.24 Number of scatterers: 15567 At special positions: 0 Unit cell: (132.66, 127.635, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 290 15.00 O 3515 8.00 N 2815 7.00 C 8921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.02 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 1.07 Conformation dependent library (CDL) restraints added in 528.9 milliseconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2254 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 46.1% alpha, 20.3% beta 137 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.723A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.598A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.646A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.276A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.566A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.702A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.724A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.599A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.647A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.807A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.526A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.735A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.825A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.660A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.668A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.521A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.179A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.719A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.905A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.708A pdb=" N VAL M 101 " --> pdb=" O CYS M 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.606A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.725A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 163 through 164 removed outlier: 4.158A pdb=" N PHE M 229 " --> pdb=" O CYS M 181 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 168 through 171 removed outlier: 3.944A pdb=" N GLU M 263 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 171 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 168 through 171 removed outlier: 3.944A pdb=" N GLU M 263 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 171 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 28 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.447A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.447A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 39 through 40 removed outlier: 3.553A pdb=" N VAL N 40 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 163 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AC5, first strand: chain 'N' and resid 177 through 180 removed outlier: 3.611A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.543A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3679 1.34 - 1.46: 5588 1.46 - 1.58: 6571 1.58 - 1.71: 578 1.71 - 1.83: 42 Bond restraints: 16458 Sorted by residual: bond pdb=" CG1 ILE A 132 " pdb=" CD1 ILE A 132 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CG1 ILE E 132 " pdb=" CD1 ILE E 132 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.32e+00 bond pdb=" C3' DG J 93 " pdb=" O3' DG J 93 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.19e+00 bond pdb=" CG LEU A 112 " pdb=" CD2 LEU A 112 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.05e+00 ... (remaining 16453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 23032 2.46 - 4.91: 405 4.91 - 7.37: 33 7.37 - 9.83: 9 9.83 - 12.29: 1 Bond angle restraints: 23480 Sorted by residual: angle pdb=" C TYR M 208 " pdb=" N ALA M 209 " pdb=" CA ALA M 209 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C TYR N 208 " pdb=" N ALA N 209 " pdb=" CA ALA N 209 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLU N 251 " pdb=" N SER N 252 " pdb=" CA SER N 252 " ideal model delta sigma weight residual 120.06 124.78 -4.72 1.19e+00 7.06e-01 1.57e+01 angle pdb=" C3' DG J 93 " pdb=" O3' DG J 93 " pdb=" P DA J 94 " ideal model delta sigma weight residual 120.20 125.29 -5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.86 116.55 -5.69 1.84e+00 2.95e-01 9.56e+00 ... (remaining 23475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 7721 35.86 - 71.72: 1463 71.72 - 107.57: 15 107.57 - 143.43: 1 143.43 - 179.29: 1 Dihedral angle restraints: 9201 sinusoidal: 5679 harmonic: 3522 Sorted by residual: dihedral pdb=" CA ASP N 186 " pdb=" C ASP N 186 " pdb=" N ILE N 187 " pdb=" CA ILE N 187 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYS H 46 " pdb=" C LYS H 46 " pdb=" N GLN H 47 " pdb=" CA GLN H 47 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLU M 251 " pdb=" C GLU M 251 " pdb=" N SER M 252 " pdb=" CA SER M 252 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 9198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1662 0.040 - 0.079: 692 0.079 - 0.119: 213 0.119 - 0.159: 58 0.159 - 0.198: 16 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CB THR G 101 " pdb=" CA THR G 101 " pdb=" OG1 THR G 101 " pdb=" CG2 THR G 101 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CG LEU A 94 " pdb=" CB LEU A 94 " pdb=" CD1 LEU A 94 " pdb=" CD2 LEU A 94 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA LYS H 46 " pdb=" N LYS H 46 " pdb=" C LYS H 46 " pdb=" CB LYS H 46 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2638 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 74 " -0.024 2.00e-02 2.50e+03 1.85e-02 6.82e+00 pdb=" CG TYR M 74 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR M 74 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR M 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR M 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 74 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR M 74 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 74 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 74 " 0.024 2.00e-02 2.50e+03 1.83e-02 6.73e+00 pdb=" CG TYR N 74 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR N 74 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR N 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 74 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR N 74 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR N 74 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 74 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.019 2.00e-02 2.50e+03 1.95e-02 6.65e+00 pdb=" CG PHE G 25 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2999 2.78 - 3.31: 12515 3.31 - 3.84: 30175 3.84 - 4.37: 36172 4.37 - 4.90: 52624 Nonbonded interactions: 134485 Sorted by model distance: nonbonded pdb=" OG SER M 165 " pdb=" OG1 THR M 180 " model vdw 2.253 3.040 nonbonded pdb=" OG SER D 32 " pdb=" OP1 DT J 103 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR E 79 " pdb=" O VAL E 82 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" O VAL A 82 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.292 3.040 ... (remaining 134480 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 23 through 141 or resid 157 through 265)) selection = (chain 'N' and (resid 23 through 141 or resid 157 through 265)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.007 0.085 16462 Z= 0.286 Angle : 0.853 12.286 23488 Z= 0.490 Chirality : 0.049 0.198 2641 Planarity : 0.007 0.057 1956 Dihedral : 25.474 179.291 6935 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -2.18 (0.20), residues: 1196 helix: -1.22 (0.17), residues: 514 sheet: -0.66 (0.35), residues: 237 loop : -1.99 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG E 118 TYR 0.045 0.003 TYR M 74 PHE 0.045 0.004 PHE G 25 TRP 0.041 0.003 TRP M 132 HIS 0.016 0.003 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00680 (16458) covalent geometry : angle 0.85240 (23480) SS BOND : bond 0.00521 ( 4) SS BOND : angle 1.70447 ( 8) hydrogen bonds : bond 0.11392 ( 845) hydrogen bonds : angle 4.83185 ( 2132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7109 (tm-30) REVERT: N 112 ASP cc_start: 0.7859 (m-30) cc_final: 0.7571 (m-30) REVERT: N 185 GLN cc_start: 0.8598 (mt0) cc_final: 0.8340 (mt0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.9746 time to fit residues: 280.8957 Evaluate side-chains 191 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN D 63 ASN D 84 ASN D 95 GLN E 127 GLN H 84 ASN N 134 GLN N 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101271 restraints weight = 19000.951| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.48 r_work: 0.2956 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16462 Z= 0.169 Angle : 0.626 9.523 23488 Z= 0.362 Chirality : 0.036 0.171 2641 Planarity : 0.005 0.048 1956 Dihedral : 29.509 176.612 4618 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.63 % Allowed : 11.20 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1196 helix: 0.83 (0.20), residues: 520 sheet: -0.22 (0.35), residues: 225 loop : -1.43 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 219 TYR 0.020 0.001 TYR M 74 PHE 0.013 0.002 PHE C 25 TRP 0.013 0.001 TRP M 132 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00375 (16458) covalent geometry : angle 0.62547 (23480) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.24099 ( 8) hydrogen bonds : bond 0.04296 ( 845) hydrogen bonds : angle 3.68904 ( 2132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8573 (ttpt) REVERT: C 36 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8830 (mptm) REVERT: C 91 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: C 99 ARG cc_start: 0.8818 (mpp80) cc_final: 0.8580 (mtp85) REVERT: E 137 GLU cc_start: 0.7239 (tt0) cc_final: 0.6966 (tt0) REVERT: H 57 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8591 (mmtp) REVERT: M 25 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: M 109 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7361 (p) REVERT: M 111 GLU cc_start: 0.7475 (pm20) cc_final: 0.7076 (pp20) REVERT: M 112 ASP cc_start: 0.7809 (m-30) cc_final: 0.7527 (m-30) REVERT: M 237 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: N 158 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7646 (tpp) REVERT: N 173 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8383 (tt) outliers start: 27 outliers final: 6 residues processed: 230 average time/residue: 0.9148 time to fit residues: 224.2050 Evaluate side-chains 203 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 N 134 GLN N 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098629 restraints weight = 19117.327| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.46 r_work: 0.2919 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16462 Z= 0.198 Angle : 0.616 7.250 23488 Z= 0.356 Chirality : 0.037 0.161 2641 Planarity : 0.005 0.044 1956 Dihedral : 29.474 174.702 4618 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.31 % Allowed : 12.46 % Favored : 84.23 % 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: 0.65 (0.24), residues: 1196 helix: 1.79 (0.22), residues: 520 sheet: 0.13 (0.36), residues: 222 loop : -1.01 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 118 TYR 0.017 0.002 TYR N 74 PHE 0.021 0.002 PHE C 25 TRP 0.015 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00456 (16458) covalent geometry : angle 0.61522 (23480) SS BOND : bond 0.00454 ( 4) SS BOND : angle 1.19015 ( 8) hydrogen bonds : bond 0.04139 ( 845) hydrogen bonds : angle 3.41971 ( 2132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8568 (ttpt) REVERT: C 36 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8825 (mptm) REVERT: C 91 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: C 99 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8564 (mtp85) REVERT: E 108 ASP cc_start: 0.8935 (m-30) cc_final: 0.8729 (m-30) REVERT: M 23 GLU cc_start: 0.7892 (pm20) cc_final: 0.7672 (pm20) REVERT: M 109 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7436 (p) REVERT: M 111 GLU cc_start: 0.7439 (pm20) cc_final: 0.7157 (pp20) REVERT: M 112 ASP cc_start: 0.7959 (m-30) cc_final: 0.7692 (m-30) REVERT: M 219 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7515 (ptm160) REVERT: M 237 GLU cc_start: 0.7813 (mp0) cc_final: 0.7500 (mp0) REVERT: N 111 GLU cc_start: 0.7389 (pm20) cc_final: 0.7092 (pm20) REVERT: N 112 ASP cc_start: 0.7708 (m-30) cc_final: 0.7469 (m-30) REVERT: N 158 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7592 (tpp) REVERT: N 263 GLU cc_start: 0.6886 (mp0) cc_final: 0.6568 (mp0) outliers start: 34 outliers final: 9 residues processed: 220 average time/residue: 0.9342 time to fit residues: 218.6318 Evaluate side-chains 195 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 127 GLN N 134 GLN N 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099332 restraints weight = 18935.232| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.45 r_work: 0.2927 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16462 Z= 0.167 Angle : 0.596 9.866 23488 Z= 0.345 Chirality : 0.036 0.142 2641 Planarity : 0.004 0.043 1956 Dihedral : 29.375 174.105 4618 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.73 % Allowed : 14.90 % Favored : 82.38 % 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: 0.96 (0.24), residues: 1196 helix: 2.07 (0.22), residues: 529 sheet: 0.15 (0.37), residues: 216 loop : -0.85 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 120 TYR 0.012 0.001 TYR N 74 PHE 0.012 0.001 PHE C 25 TRP 0.010 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (16458) covalent geometry : angle 0.59563 (23480) SS BOND : bond 0.00409 ( 4) SS BOND : angle 1.03835 ( 8) hydrogen bonds : bond 0.03840 ( 845) hydrogen bonds : angle 3.35974 ( 2132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.463 Fit side-chains REVERT: B 91 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8571 (ttpt) REVERT: C 36 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8824 (mptm) REVERT: C 91 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: C 99 ARG cc_start: 0.8812 (mpp80) cc_final: 0.8565 (mtp85) REVERT: D 34 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7584 (mtmp) REVERT: G 91 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: M 109 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7389 (p) REVERT: M 169 MET cc_start: 0.7140 (mtp) cc_final: 0.6737 (ptp) REVERT: M 219 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7718 (ptm-80) REVERT: M 237 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: N 111 GLU cc_start: 0.7333 (pm20) cc_final: 0.7019 (pm20) REVERT: N 112 ASP cc_start: 0.7805 (m-30) cc_final: 0.7534 (m-30) REVERT: N 158 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: N 185 GLN cc_start: 0.8876 (mt0) cc_final: 0.8666 (tt0) REVERT: N 263 GLU cc_start: 0.6861 (mp0) cc_final: 0.6562 (mp0) outliers start: 28 outliers final: 13 residues processed: 204 average time/residue: 0.9631 time to fit residues: 209.2100 Evaluate side-chains 207 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 179 ILE Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098198 restraints weight = 18955.016| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.46 r_work: 0.2914 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16462 Z= 0.195 Angle : 0.615 21.922 23488 Z= 0.349 Chirality : 0.037 0.145 2641 Planarity : 0.005 0.044 1956 Dihedral : 29.321 173.377 4618 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.12 % Allowed : 15.09 % Favored : 81.79 % 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: 1.11 (0.24), residues: 1196 helix: 2.17 (0.22), residues: 527 sheet: 0.30 (0.36), residues: 221 loop : -0.79 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 80 TYR 0.012 0.001 TYR C 57 PHE 0.015 0.002 PHE C 25 TRP 0.012 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00447 (16458) covalent geometry : angle 0.61481 (23480) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.08594 ( 8) hydrogen bonds : bond 0.03975 ( 845) hydrogen bonds : angle 3.29599 ( 2132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.511 Fit side-chains REVERT: A 53 LYS cc_start: 0.9233 (ttpp) cc_final: 0.9016 (ttmt) REVERT: B 91 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8570 (ttpt) REVERT: C 36 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8802 (mptm) REVERT: C 41 GLU cc_start: 0.8780 (tt0) cc_final: 0.8526 (tm-30) REVERT: C 99 ARG cc_start: 0.8810 (mpp80) cc_final: 0.8560 (mtp85) REVERT: G 91 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: M 105 LEU cc_start: 0.8852 (mt) cc_final: 0.8603 (mt) REVERT: M 109 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7397 (p) REVERT: M 219 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7958 (ptm-80) REVERT: N 111 GLU cc_start: 0.7454 (pm20) cc_final: 0.7197 (pm20) REVERT: N 112 ASP cc_start: 0.7917 (m-30) cc_final: 0.7616 (m-30) REVERT: N 185 GLN cc_start: 0.8836 (mt0) cc_final: 0.8557 (tt0) REVERT: N 263 GLU cc_start: 0.6925 (mp0) cc_final: 0.6592 (mp0) outliers start: 32 outliers final: 9 residues processed: 209 average time/residue: 0.9954 time to fit residues: 221.4477 Evaluate side-chains 201 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 25 GLN N 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098328 restraints weight = 18959.537| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.46 r_work: 0.2935 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16462 Z= 0.188 Angle : 0.613 21.542 23488 Z= 0.347 Chirality : 0.036 0.150 2641 Planarity : 0.005 0.052 1956 Dihedral : 29.296 173.164 4618 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.53 % Allowed : 16.26 % Favored : 81.21 % 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: 1.20 (0.24), residues: 1196 helix: 2.24 (0.22), residues: 527 sheet: 0.36 (0.37), residues: 218 loop : -0.73 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 80 TYR 0.012 0.001 TYR C 57 PHE 0.012 0.001 PHE C 25 TRP 0.009 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00430 (16458) covalent geometry : angle 0.61238 (23480) SS BOND : bond 0.00363 ( 4) SS BOND : angle 0.96257 ( 8) hydrogen bonds : bond 0.03893 ( 845) hydrogen bonds : angle 3.28664 ( 2132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9226 (ttpp) cc_final: 0.9004 (ttmt) REVERT: B 91 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8575 (ttpt) REVERT: C 36 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8774 (mptm) REVERT: C 41 GLU cc_start: 0.8776 (tt0) cc_final: 0.8515 (tm-30) REVERT: C 99 ARG cc_start: 0.8796 (mpp80) cc_final: 0.8545 (mtp85) REVERT: G 91 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: M 25 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: M 105 LEU cc_start: 0.8861 (mt) cc_final: 0.8618 (mt) REVERT: M 109 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7423 (p) REVERT: M 169 MET cc_start: 0.7500 (mtp) cc_final: 0.6997 (ptp) REVERT: M 219 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7922 (ptm-80) REVERT: N 111 GLU cc_start: 0.7464 (pm20) cc_final: 0.7194 (pm20) REVERT: N 112 ASP cc_start: 0.7949 (m-30) cc_final: 0.7642 (m-30) REVERT: N 158 MET cc_start: 0.7792 (tpp) cc_final: 0.7334 (tpp) REVERT: N 169 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7145 (mtt) REVERT: N 263 GLU cc_start: 0.6886 (mp0) cc_final: 0.6202 (mp0) outliers start: 26 outliers final: 11 residues processed: 204 average time/residue: 0.9704 time to fit residues: 210.5368 Evaluate side-chains 202 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 169 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 25 GLN N 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099475 restraints weight = 18875.963| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.46 r_work: 0.2936 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16462 Z= 0.149 Angle : 0.603 21.862 23488 Z= 0.342 Chirality : 0.035 0.145 2641 Planarity : 0.004 0.072 1956 Dihedral : 29.270 173.519 4618 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.85 % Allowed : 17.04 % Favored : 81.11 % 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: 1.36 (0.24), residues: 1196 helix: 2.42 (0.22), residues: 527 sheet: 0.32 (0.37), residues: 215 loop : -0.63 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 80 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (16458) covalent geometry : angle 0.60300 (23480) SS BOND : bond 0.00428 ( 4) SS BOND : angle 1.01205 ( 8) hydrogen bonds : bond 0.03613 ( 845) hydrogen bonds : angle 3.25675 ( 2132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9228 (ttpp) cc_final: 0.9014 (ttmt) REVERT: B 91 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8566 (ttpt) REVERT: C 36 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8783 (mptm) REVERT: C 41 GLU cc_start: 0.8768 (tt0) cc_final: 0.8505 (tm-30) REVERT: C 99 ARG cc_start: 0.8784 (mpp80) cc_final: 0.8530 (mtp85) REVERT: G 91 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: M 25 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: M 105 LEU cc_start: 0.8902 (mt) cc_final: 0.8674 (mt) REVERT: M 109 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7394 (p) REVERT: M 169 MET cc_start: 0.7520 (mtp) cc_final: 0.7057 (ptp) REVERT: M 219 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.6879 (ptm-80) REVERT: M 237 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: N 111 GLU cc_start: 0.7474 (pm20) cc_final: 0.7215 (pm20) REVERT: N 112 ASP cc_start: 0.7901 (m-30) cc_final: 0.7585 (m-30) REVERT: N 169 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7213 (mtt) REVERT: N 263 GLU cc_start: 0.6934 (mp0) cc_final: 0.6220 (mp0) outliers start: 19 outliers final: 9 residues processed: 196 average time/residue: 0.9646 time to fit residues: 200.8151 Evaluate side-chains 199 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 169 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS E 127 GLN N 134 GLN N 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.095681 restraints weight = 18819.570| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.51 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16462 Z= 0.278 Angle : 0.671 22.010 23488 Z= 0.375 Chirality : 0.040 0.146 2641 Planarity : 0.005 0.046 1956 Dihedral : 29.567 171.167 4618 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.82 % Allowed : 16.65 % Favored : 80.53 % 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: 1.09 (0.24), residues: 1196 helix: 2.02 (0.22), residues: 535 sheet: 0.23 (0.35), residues: 237 loop : -0.63 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 80 TYR 0.016 0.002 TYR G 57 PHE 0.016 0.002 PHE G 25 TRP 0.011 0.002 TRP M 132 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00648 (16458) covalent geometry : angle 0.67071 (23480) SS BOND : bond 0.00528 ( 4) SS BOND : angle 1.20824 ( 8) hydrogen bonds : bond 0.04670 ( 845) hydrogen bonds : angle 3.37848 ( 2132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.475 Fit side-chains REVERT: B 91 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8620 (ttpt) REVERT: C 36 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8798 (mptm) REVERT: C 41 GLU cc_start: 0.8841 (tt0) cc_final: 0.8549 (tm-30) REVERT: C 99 ARG cc_start: 0.8841 (mpp80) cc_final: 0.8606 (mtp85) REVERT: G 91 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: M 105 LEU cc_start: 0.8931 (mt) cc_final: 0.8706 (mt) REVERT: M 109 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7204 (p) REVERT: M 112 ASP cc_start: 0.8140 (m-30) cc_final: 0.7904 (m-30) REVERT: M 169 MET cc_start: 0.7604 (mtp) cc_final: 0.7047 (ptp) REVERT: M 219 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8015 (ptm-80) REVERT: N 111 GLU cc_start: 0.7550 (pm20) cc_final: 0.7246 (pm20) REVERT: N 112 ASP cc_start: 0.8109 (m-30) cc_final: 0.7813 (m-30) REVERT: N 158 MET cc_start: 0.7807 (tpp) cc_final: 0.7412 (tmm) REVERT: N 263 GLU cc_start: 0.7014 (mp0) cc_final: 0.6322 (mp0) outliers start: 29 outliers final: 11 residues processed: 197 average time/residue: 0.9840 time to fit residues: 206.0626 Evaluate side-chains 195 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098299 restraints weight = 18902.360| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.46 r_work: 0.2916 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16462 Z= 0.155 Angle : 0.624 22.216 23488 Z= 0.353 Chirality : 0.036 0.141 2641 Planarity : 0.004 0.063 1956 Dihedral : 29.471 172.810 4618 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.36 % Allowed : 17.62 % Favored : 81.01 % 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: 1.33 (0.24), residues: 1196 helix: 2.34 (0.22), residues: 528 sheet: 0.35 (0.36), residues: 221 loop : -0.63 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 80 TYR 0.011 0.001 TYR N 74 PHE 0.008 0.001 PHE H 70 TRP 0.007 0.001 TRP M 132 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (16458) covalent geometry : angle 0.62385 (23480) SS BOND : bond 0.00426 ( 4) SS BOND : angle 0.93968 ( 8) hydrogen bonds : bond 0.03801 ( 845) hydrogen bonds : angle 3.29558 ( 2132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.468 Fit side-chains REVERT: B 91 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8577 (ttpt) REVERT: C 36 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8783 (mptm) REVERT: C 41 GLU cc_start: 0.8806 (tt0) cc_final: 0.8523 (tm-30) REVERT: C 99 ARG cc_start: 0.8800 (mpp80) cc_final: 0.8552 (mtp85) REVERT: G 91 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: M 109 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7089 (p) REVERT: M 112 ASP cc_start: 0.8039 (m-30) cc_final: 0.7807 (m-30) REVERT: M 169 MET cc_start: 0.7621 (mtp) cc_final: 0.6958 (ptp) REVERT: M 219 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (ptm-80) REVERT: N 111 GLU cc_start: 0.7530 (pm20) cc_final: 0.7247 (pm20) REVERT: N 112 ASP cc_start: 0.8079 (m-30) cc_final: 0.7765 (m-30) REVERT: N 158 MET cc_start: 0.7795 (tpp) cc_final: 0.7427 (tmm) REVERT: N 169 MET cc_start: 0.7696 (mtt) cc_final: 0.7487 (mtt) REVERT: N 263 GLU cc_start: 0.7023 (mp0) cc_final: 0.6309 (mp0) outliers start: 14 outliers final: 8 residues processed: 198 average time/residue: 1.0020 time to fit residues: 210.8647 Evaluate side-chains 196 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096471 restraints weight = 18889.080| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.47 r_work: 0.2889 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16462 Z= 0.236 Angle : 0.650 20.564 23488 Z= 0.365 Chirality : 0.038 0.139 2641 Planarity : 0.005 0.053 1956 Dihedral : 29.414 171.552 4618 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.46 % Allowed : 17.92 % Favored : 80.62 % 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: 1.27 (0.24), residues: 1196 helix: 2.22 (0.22), residues: 528 sheet: 0.33 (0.35), residues: 234 loop : -0.57 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 80 TYR 0.014 0.002 TYR C 57 PHE 0.014 0.002 PHE G 25 TRP 0.010 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00549 (16458) covalent geometry : angle 0.64945 (23480) SS BOND : bond 0.00492 ( 4) SS BOND : angle 1.29500 ( 8) hydrogen bonds : bond 0.04320 ( 845) hydrogen bonds : angle 3.30432 ( 2132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.508 Fit side-chains REVERT: B 91 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8629 (ttpt) REVERT: C 36 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8765 (mptm) REVERT: C 41 GLU cc_start: 0.8829 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 99 ARG cc_start: 0.8864 (mpp80) cc_final: 0.8637 (mtp85) REVERT: E 137 GLU cc_start: 0.7487 (tt0) cc_final: 0.7209 (tt0) REVERT: G 91 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: H 76 GLU cc_start: 0.9001 (tp30) cc_final: 0.8679 (tp30) REVERT: M 109 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7222 (p) REVERT: M 112 ASP cc_start: 0.8119 (m-30) cc_final: 0.7893 (m-30) REVERT: M 169 MET cc_start: 0.7674 (mtp) cc_final: 0.6874 (ptp) REVERT: M 219 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8011 (ptm-80) REVERT: N 111 GLU cc_start: 0.7481 (pm20) cc_final: 0.7197 (pm20) REVERT: N 112 ASP cc_start: 0.8134 (m-30) cc_final: 0.7840 (m-30) REVERT: N 158 MET cc_start: 0.7795 (tpp) cc_final: 0.7383 (tmm) REVERT: N 169 MET cc_start: 0.7773 (mtt) cc_final: 0.7384 (mtt) REVERT: N 263 GLU cc_start: 0.7093 (mp0) cc_final: 0.6378 (mp0) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 1.0206 time to fit residues: 201.5627 Evaluate side-chains 189 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 135 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098326 restraints weight = 18823.652| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.45 r_work: 0.2918 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16462 Z= 0.152 Angle : 0.625 20.492 23488 Z= 0.353 Chirality : 0.036 0.145 2641 Planarity : 0.005 0.066 1956 Dihedral : 29.405 171.878 4618 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.27 % Allowed : 18.31 % Favored : 80.43 % 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: 1.41 (0.24), residues: 1196 helix: 2.40 (0.22), residues: 528 sheet: 0.36 (0.36), residues: 221 loop : -0.55 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 80 TYR 0.013 0.001 TYR M 76 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP N 58 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (16458) covalent geometry : angle 0.62425 (23480) SS BOND : bond 0.00518 ( 4) SS BOND : angle 1.30336 ( 8) hydrogen bonds : bond 0.03834 ( 845) hydrogen bonds : angle 3.28765 ( 2132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7473.26 seconds wall clock time: 127 minutes 17.13 seconds (7637.13 seconds total)