Starting phenix.real_space_refine on Wed Mar 4 21:28:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhy_22340/03_2026/7jhy_22340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhy_22340/03_2026/7jhy_22340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jhy_22340/03_2026/7jhy_22340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhy_22340/03_2026/7jhy_22340.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhy_22340/03_2026/7jhy_22340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhy_22340/03_2026/7jhy_22340.cif" } resolution = 3.9 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= 0.035 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 30 5.49 5 S 6 5.16 5 C 10361 2.51 5 N 3013 2.21 5 O 3187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16597 Number of models: 1 Model: "" Number of chains: 3 Chain: "a" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'RNA': 31} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 13, 'rna3p_pur': 1, 'rna3p_pyr': 13} Link IDs: {'rna2p': 16, 'rna3p': 14} Chain: "g" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: b, c, d, e, f, h, i, j, k Time building chain proxies: 2.69, per 1000 atoms: 0.16 Number of scatterers: 16597 At special positions: 0 Unit cell: (115.5, 108.9, 189.2, 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 6 16.00 P 30 15.00 O 3187 8.00 N 3013 7.00 C 10361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 717.3 milliseconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 34.6% alpha, 9.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'e' and resid 66 through 83 removed outlier: 3.795A pdb=" N PHE e 70 " --> pdb=" O SER e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU e 125 " --> pdb=" O ASN e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 Processing helix chain 'e' and resid 232 through 248 Processing helix chain 'e' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY e 257 " --> pdb=" O SER e 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 254 through 257' Processing helix chain 'd' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE d 70 " --> pdb=" O SER d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU d 125 " --> pdb=" O ASN d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 133 Processing helix chain 'd' and resid 232 through 248 Processing helix chain 'd' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY d 257 " --> pdb=" O SER d 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 254 through 257' Processing helix chain 'c' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE c 70 " --> pdb=" O SER c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU c 125 " --> pdb=" O ASN c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 133 Processing helix chain 'c' and resid 232 through 248 Processing helix chain 'c' and resid 254 through 257 removed outlier: 3.540A pdb=" N GLY c 257 " --> pdb=" O SER c 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 254 through 257' Processing helix chain 'f' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE f 70 " --> pdb=" O SER f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU f 125 " --> pdb=" O ASN f 121 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 133 Processing helix chain 'f' and resid 232 through 248 Processing helix chain 'f' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY f 257 " --> pdb=" O SER f 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 254 through 257' Processing helix chain 'b' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE b 70 " --> pdb=" O SER b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU b 125 " --> pdb=" O ASN b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 133 Processing helix chain 'b' and resid 232 through 248 Processing helix chain 'b' and resid 254 through 257 removed outlier: 3.538A pdb=" N GLY b 257 " --> pdb=" O SER b 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 257' Processing helix chain 'a' and resid 66 through 83 removed outlier: 3.795A pdb=" N PHE a 70 " --> pdb=" O SER a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 126 removed outlier: 3.625A pdb=" N LEU a 125 " --> pdb=" O ASN a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 133 Processing helix chain 'a' and resid 232 through 248 Processing helix chain 'a' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY a 257 " --> pdb=" O SER a 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 254 through 257' Processing helix chain 'h' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG h 11 " --> pdb=" O THR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA h 34 " --> pdb=" O ALA h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 78 Processing helix chain 'h' and resid 83 through 94 Processing helix chain 'h' and resid 102 through 113 Processing helix chain 'h' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR h 122 " --> pdb=" O LEU h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 145 Processing helix chain 'g' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG g 11 " --> pdb=" O THR g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 44 removed outlier: 3.636A pdb=" N ALA g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 94 Processing helix chain 'g' and resid 102 through 113 Processing helix chain 'g' and resid 118 through 127 removed outlier: 3.729A pdb=" N THR g 122 " --> pdb=" O LEU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 145 Processing helix chain 'j' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG j 11 " --> pdb=" O THR j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA j 34 " --> pdb=" O ALA j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 78 Processing helix chain 'j' and resid 83 through 94 Processing helix chain 'j' and resid 102 through 113 Processing helix chain 'j' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 128 through 145 Processing helix chain 'k' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG k 11 " --> pdb=" O THR k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 78 Processing helix chain 'k' and resid 83 through 94 Processing helix chain 'k' and resid 102 through 113 Processing helix chain 'k' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR k 122 " --> pdb=" O LEU k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 128 through 145 Processing helix chain 'i' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG i 11 " --> pdb=" O THR i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA i 34 " --> pdb=" O ALA i 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 78 Processing helix chain 'i' and resid 83 through 94 Processing helix chain 'i' and resid 102 through 113 Processing helix chain 'i' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR i 122 " --> pdb=" O LEU i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 128 through 145 Processing sheet with id=AA1, first strand: chain 'e' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG e 253 " --> pdb=" O HIS e 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN e 260 " --> pdb=" O GLY e 251 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N GLY e 251 " --> pdb=" O GLN e 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR e 262 " --> pdb=" O HIS e 249 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N HIS e 249 " --> pdb=" O THR e 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'd' and resid 145 through 147 removed outlier: 4.123A pdb=" N ARG d 253 " --> pdb=" O HIS d 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN d 260 " --> pdb=" O GLY d 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY d 251 " --> pdb=" O GLN d 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR d 262 " --> pdb=" O HIS d 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS d 249 " --> pdb=" O THR d 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 50 through 53 Processing sheet with id=AA5, first strand: chain 'c' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG c 253 " --> pdb=" O HIS c 258 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLN c 260 " --> pdb=" O GLY c 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY c 251 " --> pdb=" O GLN c 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR c 262 " --> pdb=" O HIS c 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS c 249 " --> pdb=" O THR c 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 50 through 53 Processing sheet with id=AA7, first strand: chain 'f' and resid 145 through 147 removed outlier: 4.123A pdb=" N ARG f 253 " --> pdb=" O HIS f 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN f 260 " --> pdb=" O GLY f 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY f 251 " --> pdb=" O GLN f 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR f 262 " --> pdb=" O HIS f 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS f 249 " --> pdb=" O THR f 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 50 through 53 Processing sheet with id=AA9, first strand: chain 'b' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG b 253 " --> pdb=" O HIS b 258 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLN b 260 " --> pdb=" O GLY b 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY b 251 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR b 262 " --> pdb=" O HIS b 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS b 249 " --> pdb=" O THR b 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 50 through 53 Processing sheet with id=AB2, first strand: chain 'a' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG a 253 " --> pdb=" O HIS a 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN a 260 " --> pdb=" O GLY a 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY a 251 " --> pdb=" O GLN a 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR a 262 " --> pdb=" O HIS a 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS a 249 " --> pdb=" O THR a 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 50 through 53 548 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4402 1.33 - 1.45: 2903 1.45 - 1.57: 9609 1.57 - 1.68: 60 1.68 - 1.80: 12 Bond restraints: 16986 Sorted by residual: bond pdb=" C ASP k 58 " pdb=" N PRO k 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.98e+00 bond pdb=" C ASP i 58 " pdb=" N PRO i 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" C ASP j 58 " pdb=" N PRO j 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.90e+00 bond pdb=" C THR d 168 " pdb=" N PRO d 169 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.89e+00 bond pdb=" C ASP h 58 " pdb=" N PRO h 59 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 ... (remaining 16981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 22295 2.39 - 4.78: 747 4.78 - 7.17: 161 7.17 - 9.56: 58 9.56 - 11.95: 22 Bond angle restraints: 23283 Sorted by residual: angle pdb=" N PRO j 116 " pdb=" CA PRO j 116 " pdb=" CB PRO j 116 " ideal model delta sigma weight residual 103.26 109.92 -6.66 1.14e+00 7.69e-01 3.41e+01 angle pdb=" N PRO h 116 " pdb=" CA PRO h 116 " pdb=" CB PRO h 116 " ideal model delta sigma weight residual 103.26 109.90 -6.64 1.14e+00 7.69e-01 3.39e+01 angle pdb=" N PRO k 116 " pdb=" CA PRO k 116 " pdb=" CB PRO k 116 " ideal model delta sigma weight residual 103.26 109.88 -6.62 1.14e+00 7.69e-01 3.37e+01 angle pdb=" N PRO i 116 " pdb=" CA PRO i 116 " pdb=" CB PRO i 116 " ideal model delta sigma weight residual 103.26 109.87 -6.61 1.14e+00 7.69e-01 3.37e+01 angle pdb=" N PRO g 116 " pdb=" CA PRO g 116 " pdb=" CB PRO g 116 " ideal model delta sigma weight residual 103.26 109.85 -6.59 1.14e+00 7.69e-01 3.34e+01 ... (remaining 23278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 9957 35.63 - 71.26: 276 71.26 - 106.89: 30 106.89 - 142.52: 3 142.52 - 178.15: 4 Dihedral angle restraints: 10270 sinusoidal: 4320 harmonic: 5950 Sorted by residual: dihedral pdb=" O4' U z 8 " pdb=" C1' U z 8 " pdb=" N1 U z 8 " pdb=" C2 U z 8 " ideal model delta sinusoidal sigma weight residual 232.00 53.85 178.15 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U z 3 " pdb=" C1' U z 3 " pdb=" N1 U z 3 " pdb=" C2 U z 3 " ideal model delta sinusoidal sigma weight residual 232.00 59.09 172.91 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U z 31 " pdb=" C1' U z 31 " pdb=" N1 U z 31 " pdb=" C2 U z 31 " ideal model delta sinusoidal sigma weight residual -128.00 35.51 -163.51 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 10267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2099 0.061 - 0.122: 568 0.122 - 0.183: 67 0.183 - 0.244: 31 0.244 - 0.305: 1 Chirality restraints: 2766 Sorted by residual: chirality pdb=" C3' A z 1 " pdb=" C4' A z 1 " pdb=" O3' A z 1 " pdb=" C2' A z 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ARG b 276 " pdb=" N ARG b 276 " pdb=" C ARG b 276 " pdb=" CB ARG b 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG f 276 " pdb=" N ARG f 276 " pdb=" C ARG f 276 " pdb=" CB ARG f 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2763 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU b 161 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO b 162 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO b 162 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO b 162 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU f 161 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO f 162 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO f 162 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO f 162 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU a 161 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO a 162 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO a 162 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO a 162 " -0.041 5.00e-02 4.00e+02 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 913 2.73 - 3.27: 15867 3.27 - 3.81: 25430 3.81 - 4.36: 27686 4.36 - 4.90: 48153 Nonbonded interactions: 118049 Sorted by model distance: nonbonded pdb=" NH2 ARG h 114 " pdb=" O PRO g 18 " model vdw 2.185 3.120 nonbonded pdb=" NH2 ARG b 76 " pdb=" OP1 U z 31 " model vdw 2.295 3.120 nonbonded pdb=" NE ARG c 71 " pdb=" OP1 U z 19 " model vdw 2.320 3.120 nonbonded pdb=" NE ARG d 71 " pdb=" OP2 U z 13 " model vdw 2.357 3.120 nonbonded pdb=" O2' U z 10 " pdb=" O4' A z 11 " model vdw 2.373 3.040 ... (remaining 118044 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 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 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 : 0.005 0.061 16986 Z= 0.230 Angle : 1.144 11.948 23283 Z= 0.578 Chirality : 0.057 0.305 2766 Planarity : 0.007 0.075 2903 Dihedral : 17.137 178.149 6380 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.76 % Favored : 84.99 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.88 (0.18), residues: 2005 helix: -0.18 (0.21), residues: 613 sheet: -1.50 (0.32), residues: 264 loop : -3.19 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG i 75 TYR 0.011 0.002 TYR g 47 PHE 0.007 0.001 PHE b 237 TRP 0.019 0.002 TRP h 87 HIS 0.004 0.001 HIS f 249 Details of bonding type rmsd covalent geometry : bond 0.00485 (16986) covalent geometry : angle 1.14351 (23283) hydrogen bonds : bond 0.13702 ( 548) hydrogen bonds : angle 6.84868 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 116 ASP cc_start: 0.6625 (m-30) cc_final: 0.6311 (m-30) REVERT: c 52 ILE cc_start: 0.8850 (pt) cc_final: 0.7994 (pt) REVERT: c 59 ILE cc_start: 0.8967 (mm) cc_final: 0.8748 (tt) REVERT: f 228 ASN cc_start: 0.8034 (m110) cc_final: 0.7720 (m110) REVERT: b 29 SER cc_start: 0.8256 (m) cc_final: 0.7815 (t) REVERT: b 118 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5558 (mm-30) REVERT: b 276 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7266 (ptt90) REVERT: a 19 ARG cc_start: 0.6931 (ptm-80) cc_final: 0.6226 (ptm-80) REVERT: a 223 TRP cc_start: 0.7773 (p-90) cc_final: 0.7522 (p-90) REVERT: h 8 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6452 (tp40) REVERT: h 136 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.5900 (ttt-90) REVERT: g 104 ASP cc_start: 0.7238 (p0) cc_final: 0.6812 (p0) REVERT: g 106 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.5791 (ttp80) REVERT: j 76 ARG cc_start: 0.8297 (tmm160) cc_final: 0.8089 (tpt170) REVERT: k 80 ARG cc_start: 0.7701 (mpt90) cc_final: 0.6685 (mpt-90) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1762 time to fit residues: 107.4553 Evaluate side-chains 355 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.0670 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 32 HIS d 159 HIS b 61 GLN b 159 HIS a 159 HIS ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.223192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.182954 restraints weight = 23009.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.186091 restraints weight = 14301.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.188869 restraints weight = 10840.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.190208 restraints weight = 8494.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.191260 restraints weight = 7389.731| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16986 Z= 0.212 Angle : 0.860 12.905 23283 Z= 0.423 Chirality : 0.048 0.255 2766 Planarity : 0.007 0.098 2903 Dihedral : 15.866 176.043 2718 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.81 % Favored : 84.19 % Rotamer: Outliers : 1.99 % Allowed : 15.10 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.49 (0.19), residues: 2005 helix: 0.45 (0.21), residues: 619 sheet: -1.31 (0.33), residues: 264 loop : -3.15 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG h 106 TYR 0.016 0.002 TYR j 47 PHE 0.023 0.002 PHE d 70 TRP 0.039 0.002 TRP c 281 HIS 0.007 0.002 HIS d 159 Details of bonding type rmsd covalent geometry : bond 0.00480 (16986) covalent geometry : angle 0.85989 (23283) hydrogen bonds : bond 0.04533 ( 548) hydrogen bonds : angle 5.49603 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 141 MET cc_start: 0.7042 (mmp) cc_final: 0.6767 (mmp) REVERT: e 226 LEU cc_start: 0.8134 (mt) cc_final: 0.7908 (mt) REVERT: d 118 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5562 (pm20) REVERT: d 120 ARG cc_start: 0.5256 (mtm180) cc_final: 0.3832 (mtm180) REVERT: d 153 GLU cc_start: 0.6072 (tp30) cc_final: 0.5771 (tp30) REVERT: c 52 ILE cc_start: 0.8560 (pt) cc_final: 0.8274 (pt) REVERT: c 59 ILE cc_start: 0.9040 (mm) cc_final: 0.8776 (tt) REVERT: b 29 SER cc_start: 0.8432 (m) cc_final: 0.7829 (t) REVERT: b 141 MET cc_start: 0.7855 (mmm) cc_final: 0.7625 (mtt) REVERT: b 254 SER cc_start: 0.8843 (p) cc_final: 0.8123 (t) REVERT: a 19 ARG cc_start: 0.7084 (ptm-80) cc_final: 0.6271 (ptm-80) REVERT: a 223 TRP cc_start: 0.7821 (p-90) cc_final: 0.7519 (p-90) REVERT: h 8 GLN cc_start: 0.7277 (mm-40) cc_final: 0.7046 (tp40) REVERT: h 44 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (tt) REVERT: h 107 LEU cc_start: 0.8932 (tp) cc_final: 0.8593 (mt) REVERT: h 122 THR cc_start: 0.7307 (p) cc_final: 0.7073 (t) REVERT: h 136 ARG cc_start: 0.7882 (ttt-90) cc_final: 0.6479 (ttt-90) REVERT: g 104 ASP cc_start: 0.6972 (p0) cc_final: 0.6628 (p0) REVERT: g 106 ARG cc_start: 0.6643 (ttp-110) cc_final: 0.5735 (ttp80) REVERT: j 47 TYR cc_start: 0.7055 (m-80) cc_final: 0.6703 (m-10) REVERT: j 109 LEU cc_start: 0.8785 (tp) cc_final: 0.8519 (tt) REVERT: k 103 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7320 (mtp180) outliers start: 33 outliers final: 24 residues processed: 393 average time/residue: 0.1649 time to fit residues: 92.5148 Evaluate side-chains 380 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 354 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 254 SER Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 287 ASP Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 74 VAL Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 147 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 232 HIS f 32 HIS f 159 HIS f 228 ASN b 32 HIS ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.226452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.186450 restraints weight = 23209.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.190638 restraints weight = 14371.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.192133 restraints weight = 10631.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.194010 restraints weight = 8974.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.195667 restraints weight = 7502.598| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16986 Z= 0.146 Angle : 0.785 10.911 23283 Z= 0.379 Chirality : 0.045 0.274 2766 Planarity : 0.005 0.049 2903 Dihedral : 15.688 177.476 2718 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 3.01 % Allowed : 19.01 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.29 (0.19), residues: 2005 helix: 0.77 (0.21), residues: 619 sheet: -1.24 (0.32), residues: 264 loop : -3.13 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 139 TYR 0.011 0.001 TYR j 47 PHE 0.017 0.001 PHE d 70 TRP 0.017 0.001 TRP c 281 HIS 0.004 0.001 HIS d 159 Details of bonding type rmsd covalent geometry : bond 0.00323 (16986) covalent geometry : angle 0.78470 (23283) hydrogen bonds : bond 0.03895 ( 548) hydrogen bonds : angle 5.14598 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 354 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 70 PHE cc_start: 0.8978 (t80) cc_final: 0.8714 (t80) REVERT: c 59 ILE cc_start: 0.9073 (mm) cc_final: 0.8757 (tt) REVERT: f 236 PHE cc_start: 0.8420 (t80) cc_final: 0.8219 (t80) REVERT: b 29 SER cc_start: 0.8410 (m) cc_final: 0.7820 (t) REVERT: b 254 SER cc_start: 0.8836 (p) cc_final: 0.8180 (t) REVERT: a 48 ARG cc_start: 0.6424 (tpt-90) cc_final: 0.5851 (tpt-90) REVERT: a 141 MET cc_start: 0.7687 (mmm) cc_final: 0.7165 (mmm) REVERT: h 8 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6821 (tp40) REVERT: h 44 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7731 (tt) REVERT: h 122 THR cc_start: 0.7426 (p) cc_final: 0.7145 (t) REVERT: h 136 ARG cc_start: 0.7787 (ttt-90) cc_final: 0.6160 (ttt-90) REVERT: g 104 ASP cc_start: 0.6964 (p0) cc_final: 0.6667 (p0) REVERT: g 106 ARG cc_start: 0.6646 (ttp-110) cc_final: 0.5718 (ttp80) REVERT: k 47 TYR cc_start: 0.6328 (m-10) cc_final: 0.6051 (m-10) outliers start: 50 outliers final: 36 residues processed: 375 average time/residue: 0.1566 time to fit residues: 84.7826 Evaluate side-chains 372 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 335 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 66 SER Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 266 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 131 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 284 GLN c 232 HIS a 32 HIS a 61 GLN h 94 GLN g 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.218149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.178242 restraints weight = 22973.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.180232 restraints weight = 15025.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.182911 restraints weight = 11267.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.184826 restraints weight = 8954.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.185630 restraints weight = 7422.647| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16986 Z= 0.209 Angle : 0.836 10.856 23283 Z= 0.412 Chirality : 0.048 0.244 2766 Planarity : 0.007 0.157 2903 Dihedral : 15.711 178.414 2718 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.51 % Favored : 83.49 % Rotamer: Outliers : 5.90 % Allowed : 19.49 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.35 (0.19), residues: 2005 helix: 0.84 (0.21), residues: 619 sheet: -1.17 (0.32), residues: 264 loop : -3.28 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG j 125 TYR 0.018 0.002 TYR j 47 PHE 0.013 0.002 PHE b 70 TRP 0.018 0.002 TRP f 281 HIS 0.008 0.002 HIS h 46 Details of bonding type rmsd covalent geometry : bond 0.00472 (16986) covalent geometry : angle 0.83596 (23283) hydrogen bonds : bond 0.04406 ( 548) hydrogen bonds : angle 5.16499 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 340 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8570 (Cg_endo) cc_final: 0.8290 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7233 (m-10) cc_final: 0.6923 (m-10) REVERT: d 153 GLU cc_start: 0.6522 (tp30) cc_final: 0.6203 (tp30) REVERT: c 59 ILE cc_start: 0.9005 (mm) cc_final: 0.8805 (tt) REVERT: c 167 SER cc_start: 0.9032 (t) cc_final: 0.8817 (t) REVERT: f 33 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7875 (mtm-85) REVERT: f 233 GLN cc_start: 0.8673 (pm20) cc_final: 0.8185 (mp10) REVERT: b 19 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7497 (ptt-90) REVERT: b 29 SER cc_start: 0.8481 (m) cc_final: 0.7901 (t) REVERT: b 232 HIS cc_start: 0.7907 (m-70) cc_final: 0.6849 (m-70) REVERT: b 254 SER cc_start: 0.8941 (p) cc_final: 0.8309 (t) REVERT: a 56 ASP cc_start: 0.6913 (m-30) cc_final: 0.6452 (p0) REVERT: a 141 MET cc_start: 0.7971 (mmm) cc_final: 0.7392 (mmm) REVERT: h 8 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6951 (mm-40) REVERT: h 33 ARG cc_start: 0.7687 (mpt180) cc_final: 0.7239 (mpt90) REVERT: h 44 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (tt) REVERT: h 122 THR cc_start: 0.7614 (p) cc_final: 0.7305 (t) REVERT: h 136 ARG cc_start: 0.8048 (ttt-90) cc_final: 0.5970 (ttt-90) REVERT: g 104 ASP cc_start: 0.7069 (p0) cc_final: 0.6829 (p0) REVERT: g 106 ARG cc_start: 0.6762 (ttp-110) cc_final: 0.5872 (ttt-90) REVERT: k 70 LEU cc_start: 0.8683 (tp) cc_final: 0.8481 (tp) REVERT: i 80 ARG cc_start: 0.8364 (mpt180) cc_final: 0.8041 (mpt180) REVERT: i 90 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8004 (tm-30) outliers start: 98 outliers final: 64 residues processed: 387 average time/residue: 0.1531 time to fit residues: 85.9010 Evaluate side-chains 395 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 242 SER Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 265 VAL Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain g residue 10 TRP Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 144 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 284 GLN d 61 GLN c 232 HIS g 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.224604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.185368 restraints weight = 22855.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.187859 restraints weight = 14300.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.190257 restraints weight = 11297.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.191771 restraints weight = 8933.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.193374 restraints weight = 7540.782| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16986 Z= 0.176 Angle : 0.794 14.060 23283 Z= 0.388 Chirality : 0.046 0.264 2766 Planarity : 0.006 0.090 2903 Dihedral : 15.569 177.257 2718 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Rotamer: Outliers : 5.23 % Allowed : 21.54 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.25 (0.19), residues: 2005 helix: 1.00 (0.21), residues: 619 sheet: -1.06 (0.33), residues: 264 loop : -3.28 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 62 TYR 0.010 0.001 TYR j 47 PHE 0.009 0.001 PHE b 70 TRP 0.017 0.001 TRP f 281 HIS 0.006 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00397 (16986) covalent geometry : angle 0.79430 (23283) hydrogen bonds : bond 0.04050 ( 548) hydrogen bonds : angle 5.06902 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 328 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8245 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7227 (m-10) cc_final: 0.6942 (m-10) REVERT: e 285 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6217 (tt) REVERT: c 167 SER cc_start: 0.9075 (t) cc_final: 0.8872 (t) REVERT: f 33 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7574 (mtm180) REVERT: f 233 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: b 29 SER cc_start: 0.8477 (m) cc_final: 0.7923 (t) REVERT: b 231 GLU cc_start: 0.5871 (tm-30) cc_final: 0.5487 (tm-30) REVERT: b 232 HIS cc_start: 0.7652 (m-70) cc_final: 0.6963 (m-70) REVERT: b 254 SER cc_start: 0.8904 (p) cc_final: 0.8254 (t) REVERT: a 48 ARG cc_start: 0.6726 (tpt-90) cc_final: 0.6015 (tpt-90) REVERT: a 56 ASP cc_start: 0.6979 (m-30) cc_final: 0.6487 (p0) REVERT: a 141 MET cc_start: 0.7989 (mmm) cc_final: 0.7436 (mmm) REVERT: h 33 ARG cc_start: 0.7736 (mpt180) cc_final: 0.7266 (mpt90) REVERT: h 44 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7884 (tt) REVERT: h 122 THR cc_start: 0.7499 (p) cc_final: 0.7230 (t) REVERT: h 136 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.5911 (ttt-90) REVERT: g 42 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6796 (tt) REVERT: g 106 ARG cc_start: 0.6682 (ttp-110) cc_final: 0.5798 (ttt180) REVERT: i 80 ARG cc_start: 0.8333 (mpt180) cc_final: 0.8037 (mpt180) REVERT: i 90 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8067 (tm-30) outliers start: 87 outliers final: 63 residues processed: 370 average time/residue: 0.1429 time to fit residues: 77.0132 Evaluate side-chains 386 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 233 GLN Chi-restraints excluded: chain f residue 254 SER Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 265 VAL Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 42 LEU Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 112 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.224306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.185034 restraints weight = 22880.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.186748 restraints weight = 15602.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.189911 restraints weight = 11519.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.191265 restraints weight = 9235.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.192589 restraints weight = 7813.600| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16986 Z= 0.144 Angle : 0.760 12.032 23283 Z= 0.368 Chirality : 0.045 0.242 2766 Planarity : 0.005 0.060 2903 Dihedral : 15.388 176.499 2718 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.41 % Favored : 84.59 % Rotamer: Outliers : 4.75 % Allowed : 23.47 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.13 (0.19), residues: 2005 helix: 1.05 (0.21), residues: 624 sheet: -0.90 (0.33), residues: 264 loop : -3.22 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG i 134 TYR 0.011 0.001 TYR j 47 PHE 0.012 0.001 PHE c 70 TRP 0.016 0.001 TRP f 281 HIS 0.006 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00325 (16986) covalent geometry : angle 0.76017 (23283) hydrogen bonds : bond 0.03690 ( 548) hydrogen bonds : angle 4.92366 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 328 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8640 (Cg_endo) cc_final: 0.8360 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7159 (m-10) cc_final: 0.6910 (m-10) REVERT: e 285 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6175 (tt) REVERT: c 167 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8772 (t) REVERT: f 233 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8199 (mp10) REVERT: b 29 SER cc_start: 0.8547 (m) cc_final: 0.7952 (t) REVERT: b 232 HIS cc_start: 0.7606 (m-70) cc_final: 0.7316 (m90) REVERT: b 254 SER cc_start: 0.8898 (p) cc_final: 0.8292 (t) REVERT: a 48 ARG cc_start: 0.6747 (tpt-90) cc_final: 0.6085 (tpt-90) REVERT: a 141 MET cc_start: 0.7926 (mmm) cc_final: 0.7384 (mmm) REVERT: h 33 ARG cc_start: 0.7761 (mpt180) cc_final: 0.7227 (mpt180) REVERT: h 44 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7939 (tt) REVERT: h 122 THR cc_start: 0.7509 (p) cc_final: 0.7279 (t) REVERT: g 106 ARG cc_start: 0.6585 (ttp-110) cc_final: 0.5794 (ttp-170) REVERT: g 118 LEU cc_start: 0.8427 (tp) cc_final: 0.8111 (tp) REVERT: j 76 ARG cc_start: 0.8732 (tpt170) cc_final: 0.7389 (tpt170) REVERT: k 40 ARG cc_start: 0.7480 (ttm170) cc_final: 0.7179 (ttt180) REVERT: i 90 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8105 (tm-30) outliers start: 79 outliers final: 60 residues processed: 373 average time/residue: 0.1447 time to fit residues: 78.8491 Evaluate side-chains 384 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 320 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 167 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 233 GLN Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.223453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.183553 restraints weight = 22780.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.185301 restraints weight = 15340.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.187930 restraints weight = 11901.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.189488 restraints weight = 9405.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.191290 restraints weight = 7920.069| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16986 Z= 0.220 Angle : 0.842 10.751 23283 Z= 0.416 Chirality : 0.048 0.269 2766 Planarity : 0.007 0.114 2903 Dihedral : 15.490 176.780 2718 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.61 % Favored : 83.39 % Rotamer: Outliers : 6.26 % Allowed : 23.04 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.27 (0.19), residues: 2005 helix: 0.94 (0.21), residues: 619 sheet: -0.89 (0.33), residues: 264 loop : -3.32 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG j 76 TYR 0.019 0.002 TYR j 47 PHE 0.015 0.002 PHE d 237 TRP 0.035 0.002 TRP g 87 HIS 0.007 0.002 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00497 (16986) covalent geometry : angle 0.84232 (23283) hydrogen bonds : bond 0.04388 ( 548) hydrogen bonds : angle 5.09751 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 332 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8704 (Cg_endo) cc_final: 0.8425 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7401 (m-10) cc_final: 0.7109 (m-10) REVERT: e 226 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7990 (mt) REVERT: d 128 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8991 (tp-100) REVERT: d 285 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5623 (tt) REVERT: c 59 ILE cc_start: 0.9224 (mm) cc_final: 0.8913 (tt) REVERT: f 33 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7637 (mtm180) REVERT: f 232 HIS cc_start: 0.6992 (m-70) cc_final: 0.6481 (m-70) REVERT: f 233 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: b 29 SER cc_start: 0.8527 (m) cc_final: 0.7942 (t) REVERT: b 254 SER cc_start: 0.8935 (p) cc_final: 0.8265 (t) REVERT: a 48 ARG cc_start: 0.6809 (tpt-90) cc_final: 0.6138 (tpt-90) REVERT: a 56 ASP cc_start: 0.7058 (m-30) cc_final: 0.6555 (p0) REVERT: a 126 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6794 (tt) REVERT: a 128 GLN cc_start: 0.6940 (tp40) cc_final: 0.6676 (tp40) REVERT: a 141 MET cc_start: 0.7985 (mmm) cc_final: 0.7434 (mmm) REVERT: h 33 ARG cc_start: 0.7685 (mpt180) cc_final: 0.7172 (mpt180) REVERT: h 44 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7876 (tt) REVERT: h 122 THR cc_start: 0.7673 (p) cc_final: 0.7387 (t) REVERT: g 73 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7835 (mmm160) REVERT: g 106 ARG cc_start: 0.6654 (ttp-110) cc_final: 0.5846 (ttp-170) REVERT: g 118 LEU cc_start: 0.8513 (tp) cc_final: 0.8213 (tp) REVERT: k 40 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6754 (ttm-80) outliers start: 104 outliers final: 74 residues processed: 386 average time/residue: 0.1401 time to fit residues: 79.8571 Evaluate side-chains 407 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 327 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain e residue 166 HIS Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 226 LEU Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 85 VAL Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 233 GLN Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 160 LEU Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain g residue 10 TRP Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 137 ILE Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain i residue 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 127 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.218235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.177450 restraints weight = 23050.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.179968 restraints weight = 15200.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.182457 restraints weight = 11668.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.183940 restraints weight = 9301.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.185865 restraints weight = 7785.626| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16986 Z= 0.145 Angle : 0.767 10.229 23283 Z= 0.373 Chirality : 0.045 0.270 2766 Planarity : 0.005 0.050 2903 Dihedral : 15.299 176.378 2718 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 4.63 % Allowed : 25.51 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.11 (0.19), residues: 2005 helix: 0.99 (0.21), residues: 630 sheet: 0.28 (0.36), residues: 192 loop : -3.30 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG i 75 TYR 0.013 0.001 TYR j 47 PHE 0.007 0.001 PHE c 70 TRP 0.024 0.001 TRP g 87 HIS 0.009 0.001 HIS b 232 Details of bonding type rmsd covalent geometry : bond 0.00325 (16986) covalent geometry : angle 0.76665 (23283) hydrogen bonds : bond 0.03735 ( 548) hydrogen bonds : angle 4.94486 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 341 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8683 (Cg_endo) cc_final: 0.8397 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7188 (m-10) cc_final: 0.6964 (m-10) REVERT: d 128 GLN cc_start: 0.9255 (tp-100) cc_final: 0.9042 (tp-100) REVERT: c 59 ILE cc_start: 0.9212 (mm) cc_final: 0.8873 (tt) REVERT: f 33 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7601 (mtm180) REVERT: f 232 HIS cc_start: 0.6750 (m-70) cc_final: 0.6233 (m-70) REVERT: f 233 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: b 29 SER cc_start: 0.8576 (m) cc_final: 0.7963 (t) REVERT: b 33 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7193 (tpp80) REVERT: b 52 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8405 (tt) REVERT: b 79 GLU cc_start: 0.7282 (tt0) cc_final: 0.6971 (tt0) REVERT: b 232 HIS cc_start: 0.7435 (m90) cc_final: 0.6421 (m90) REVERT: b 254 SER cc_start: 0.8894 (p) cc_final: 0.8231 (t) REVERT: a 48 ARG cc_start: 0.6767 (tpt-90) cc_final: 0.6034 (tpt-90) REVERT: a 56 ASP cc_start: 0.6988 (m-30) cc_final: 0.6518 (p0) REVERT: a 126 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6765 (tt) REVERT: a 141 MET cc_start: 0.7955 (mmm) cc_final: 0.7405 (mmm) REVERT: h 33 ARG cc_start: 0.7723 (mpt180) cc_final: 0.7148 (mpt180) REVERT: h 44 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7845 (tt) REVERT: h 122 THR cc_start: 0.7572 (p) cc_final: 0.7342 (t) REVERT: g 106 ARG cc_start: 0.6571 (ttp-110) cc_final: 0.5811 (ttp-170) REVERT: g 118 LEU cc_start: 0.8471 (tp) cc_final: 0.8210 (tp) REVERT: k 40 ARG cc_start: 0.7289 (ttm170) cc_final: 0.6685 (ttt180) REVERT: i 90 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8085 (tm-30) REVERT: i 114 ARG cc_start: 0.6371 (ptt90) cc_final: 0.6106 (ptt-90) outliers start: 77 outliers final: 58 residues processed: 386 average time/residue: 0.1383 time to fit residues: 79.0258 Evaluate side-chains 392 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 242 SER Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 85 VAL Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain f residue 233 GLN Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 241 LEU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.217766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.178125 restraints weight = 22965.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.180432 restraints weight = 14924.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.183073 restraints weight = 11134.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.184608 restraints weight = 8929.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.185514 restraints weight = 7535.014| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16986 Z= 0.150 Angle : 0.783 14.908 23283 Z= 0.379 Chirality : 0.045 0.248 2766 Planarity : 0.006 0.096 2903 Dihedral : 15.192 175.577 2718 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.41 % Favored : 84.59 % Rotamer: Outliers : 4.51 % Allowed : 25.09 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.07 (0.19), residues: 2005 helix: 1.08 (0.21), residues: 625 sheet: -0.78 (0.32), residues: 264 loop : -3.20 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG i 75 TYR 0.012 0.001 TYR j 47 PHE 0.022 0.001 PHE f 236 TRP 0.028 0.001 TRP g 87 HIS 0.006 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00340 (16986) covalent geometry : angle 0.78262 (23283) hydrogen bonds : bond 0.03724 ( 548) hydrogen bonds : angle 4.87665 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 327 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8706 (Cg_endo) cc_final: 0.8431 (Cg_exo) REVERT: d 128 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8873 (tp-100) REVERT: d 281 TRP cc_start: 0.5839 (OUTLIER) cc_final: 0.5386 (p90) REVERT: c 59 ILE cc_start: 0.9188 (mm) cc_final: 0.8872 (tt) REVERT: f 33 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7972 (mtm-85) REVERT: f 232 HIS cc_start: 0.6853 (m-70) cc_final: 0.6334 (m-70) REVERT: f 233 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: f 266 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6804 (p) REVERT: b 29 SER cc_start: 0.8597 (m) cc_final: 0.7988 (t) REVERT: b 79 GLU cc_start: 0.7275 (tt0) cc_final: 0.6949 (tt0) REVERT: b 232 HIS cc_start: 0.7470 (m90) cc_final: 0.7170 (m90) REVERT: b 254 SER cc_start: 0.8887 (p) cc_final: 0.8263 (t) REVERT: a 48 ARG cc_start: 0.6758 (tpt-90) cc_final: 0.6078 (tpt-90) REVERT: a 56 ASP cc_start: 0.7003 (m-30) cc_final: 0.6581 (p0) REVERT: a 126 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6804 (tt) REVERT: a 141 MET cc_start: 0.7890 (mmm) cc_final: 0.7364 (mmm) REVERT: h 33 ARG cc_start: 0.7777 (mpt180) cc_final: 0.7147 (mpt180) REVERT: h 44 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7758 (tt) REVERT: h 122 THR cc_start: 0.7576 (p) cc_final: 0.7332 (t) REVERT: g 106 ARG cc_start: 0.6590 (ttp-110) cc_final: 0.5835 (ttp-170) REVERT: g 118 LEU cc_start: 0.8545 (tp) cc_final: 0.8256 (tp) REVERT: i 90 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8097 (tm-30) REVERT: i 114 ARG cc_start: 0.6419 (ptt90) cc_final: 0.6217 (ptt90) outliers start: 75 outliers final: 61 residues processed: 369 average time/residue: 0.1424 time to fit residues: 77.3903 Evaluate side-chains 390 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 242 SER Chi-restraints excluded: chain d residue 281 TRP Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 85 VAL Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 141 MET Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain f residue 233 GLN Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 287 ASP Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 13 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 140 optimal weight: 0.0670 chunk 56 optimal weight: 0.0970 chunk 172 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 159 HIS e 247 HIS a 128 GLN ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.230884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.191506 restraints weight = 22817.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.194650 restraints weight = 14813.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.197198 restraints weight = 10935.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.198296 restraints weight = 8984.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.199569 restraints weight = 7900.049| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16986 Z= 0.132 Angle : 0.764 14.647 23283 Z= 0.367 Chirality : 0.044 0.281 2766 Planarity : 0.005 0.079 2903 Dihedral : 14.998 175.328 2718 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 3.31 % Allowed : 26.53 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 2005 helix: 1.12 (0.21), residues: 630 sheet: 0.37 (0.36), residues: 192 loop : -3.17 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG i 75 TYR 0.013 0.001 TYR j 47 PHE 0.017 0.001 PHE c 70 TRP 0.027 0.001 TRP g 87 HIS 0.005 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00298 (16986) covalent geometry : angle 0.76383 (23283) hydrogen bonds : bond 0.03379 ( 548) hydrogen bonds : angle 4.79384 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8668 (Cg_endo) cc_final: 0.8394 (Cg_exo) REVERT: d 281 TRP cc_start: 0.5922 (OUTLIER) cc_final: 0.5461 (p90) REVERT: c 59 ILE cc_start: 0.9197 (mm) cc_final: 0.8878 (tt) REVERT: f 33 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7957 (mtm-85) REVERT: f 233 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: f 266 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6865 (p) REVERT: b 29 SER cc_start: 0.8590 (m) cc_final: 0.7997 (t) REVERT: b 33 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7118 (tpp80) REVERT: b 232 HIS cc_start: 0.7260 (m90) cc_final: 0.6899 (m90) REVERT: b 254 SER cc_start: 0.8860 (p) cc_final: 0.8225 (t) REVERT: a 48 ARG cc_start: 0.6737 (tpt-90) cc_final: 0.6083 (tpt-90) REVERT: a 56 ASP cc_start: 0.6957 (m-30) cc_final: 0.6493 (p0) REVERT: a 126 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6706 (tt) REVERT: a 141 MET cc_start: 0.7840 (mmm) cc_final: 0.7344 (mmm) REVERT: a 284 GLN cc_start: 0.6231 (pp30) cc_final: 0.5198 (mp10) REVERT: h 33 ARG cc_start: 0.7878 (mpt180) cc_final: 0.7247 (mpt180) REVERT: g 106 ARG cc_start: 0.6529 (ttp-110) cc_final: 0.5909 (ttt-90) REVERT: g 118 LEU cc_start: 0.8508 (tp) cc_final: 0.8225 (tp) REVERT: k 29 SER cc_start: 0.7092 (m) cc_final: 0.6856 (t) REVERT: k 40 ARG cc_start: 0.7254 (ttm170) cc_final: 0.6700 (ttt180) outliers start: 55 outliers final: 41 residues processed: 364 average time/residue: 0.1429 time to fit residues: 76.2020 Evaluate side-chains 371 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 281 TRP Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain f residue 233 GLN Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 241 LEU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 112 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 128 GLN ** g 94 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 = 0.4211 r_free = 0.4211 target = 0.216374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.176710 restraints weight = 22822.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.179042 restraints weight = 14914.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.181499 restraints weight = 11054.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.183184 restraints weight = 8894.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.184269 restraints weight = 7413.862| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16986 Z= 0.172 Angle : 0.810 14.507 23283 Z= 0.393 Chirality : 0.045 0.184 2766 Planarity : 0.006 0.081 2903 Dihedral : 14.964 175.236 2718 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.66 % Favored : 84.34 % Rotamer: Outliers : 3.67 % Allowed : 26.65 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.19), residues: 2005 helix: 1.17 (0.21), residues: 619 sheet: -0.70 (0.32), residues: 264 loop : -3.10 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG i 75 TYR 0.008 0.001 TYR h 47 PHE 0.017 0.001 PHE c 70 TRP 0.028 0.001 TRP g 87 HIS 0.005 0.001 HIS f 159 Details of bonding type rmsd covalent geometry : bond 0.00394 (16986) covalent geometry : angle 0.81022 (23283) hydrogen bonds : bond 0.03914 ( 548) hydrogen bonds : angle 4.89687 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.65 seconds wall clock time: 51 minutes 9.06 seconds (3069.06 seconds total)