Starting phenix.real_space_refine on Sat Sep 12 14:58:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jhy_22340/09_2026/7jhy_22340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhy_22340/09_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_22340/09_2026/7jhy_22340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhy_22340/09_2026/7jhy_22340.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhy_22340/09_2026/7jhy_22340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhy_22340/09_2026/7jhy_22340.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jhy_22340/09_2026/7jhy_22340.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jhy_22340/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 31} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 13, 'rna3p_pur': 1, 'rna3p_pyr': 13} Link IDs: {'rna2p': 16, 'rna3p': 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 2.83, per 1000 atoms: 0.17 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: 1.41 Conformation dependent library (CDL) restraints added in 697.7 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: 1.50 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: 2.26 Time building geometry restraints manager: 1.88 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=" C3' A z 1 " pdb=" O3' A z 1 " ideal model delta sigma weight residual 1.415 1.450 -0.035 2.00e-02 2.50e+03 2.99e+00 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 ... (remaining 16981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 22193 2.39 - 4.78: 826 4.78 - 7.17: 182 7.17 - 9.56: 60 9.56 - 11.95: 22 Bond angle restraints: 23283 Sorted by residual: angle pdb=" C3' A z 1 " pdb=" O3' A z 1 " pdb=" P U z 2 " ideal model delta sigma weight residual 119.70 126.99 -7.29 1.20e+00 6.94e-01 3.69e+01 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 ... (remaining 23278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.86: 9780 32.86 - 65.71: 351 65.71 - 98.57: 33 98.57 - 131.43: 1 131.43 - 164.29: 1 Dihedral angle restraints: 10166 sinusoidal: 4216 harmonic: 5950 Sorted by residual: dihedral pdb=" C4' U z 19 " pdb=" C3' U z 19 " pdb=" C2' U z 19 " pdb=" C1' U z 19 " ideal model delta sinusoidal sigma weight residual 36.34 -42.69 79.04 1 3.10e+00 1.04e-01 8.09e+02 dihedral pdb=" C4' U z 8 " pdb=" C3' U z 8 " pdb=" C2' U z 8 " pdb=" C1' U z 8 " ideal model delta sinusoidal sigma weight residual 36.34 -42.69 79.03 1 3.10e+00 1.04e-01 8.09e+02 dihedral pdb=" C4' A z 14 " pdb=" C3' A z 14 " pdb=" C2' A z 14 " pdb=" C1' A z 14 " ideal model delta sinusoidal sigma weight residual 36.34 -40.18 76.53 1 3.10e+00 1.04e-01 7.66e+02 ... (remaining 10163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2364 0.085 - 0.170: 301 0.170 - 0.255: 74 0.255 - 0.341: 19 0.341 - 0.426: 8 Chirality restraints: 2766 Sorted by residual: chirality pdb=" P U z 2 " pdb=" OP1 U z 2 " pdb=" OP2 U z 2 " pdb=" O5' U z 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" P A z 14 " pdb=" OP1 A z 14 " pdb=" OP2 A z 14 " pdb=" O5' A z 14 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" P U z 26 " pdb=" OP1 U z 26 " pdb=" OP2 U z 26 " pdb=" O5' U z 26 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.13e+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: 1.820 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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= 0.232 Angle : 1.177 11.948 23283 Z= 0.580 Chirality : 0.069 0.426 2766 Planarity : 0.007 0.075 2903 Dihedral : 16.826 164.287 6276 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/Z covalent geometry : bond 0.00491 / 0.23 (16986) covalent geometry : angle 1.17657 / 0.58 (23283) hydrogen bonds : bond 0.13702 / 9.29 ( 548) hydrogen bonds : angle 6.84868 / 4.71 ( 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 : 0.513 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: 0.1553 time to fit residues: 95.9839 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 : 0.414 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 159 HIS f 159 HIS b 61 GLN b 159 HIS ** b 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4367 r_free = 0.4367 target = 0.232406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.193022 restraints weight = 22997.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.197031 restraints weight = 14494.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.199375 restraints weight = 10525.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.200996 restraints weight = 8403.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.201813 restraints weight = 7475.791| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16986 Z= 0.191 Angle : 1.110 28.971 23283 Z= 0.474 Chirality : 0.086 1.231 2766 Planarity : 0.006 0.062 2903 Dihedral : 12.652 168.654 2614 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.46 % Favored : 84.54 % Rotamer: Outliers : 1.62 % Allowed : 14.56 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.38 (0.22), residues: 629 sheet: -1.31 (0.33), residues: 264 loop : -3.14 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG h 106 TYR 0.013 0.001 TYR j 47 PHE 0.020 0.002 PHE d 70 TRP 0.039 0.002 TRP c 281 HIS 0.006 0.001 HIS d 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (16986) covalent geometry : angle 1.10974 / 0.47 (23283) hydrogen bonds : bond 0.04430 / 2.99 ( 548) hydrogen bonds : angle 5.49061 / 3.78 ( 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 406 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 379 time to evaluate : 0.530 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: 0.6995 (mmp) cc_final: 0.6603 (mmp) REVERT: e 226 LEU cc_start: 0.8026 (mt) cc_final: 0.7823 (mt) REVERT: d 120 ARG cc_start: 0.5405 (mtm180) cc_final: 0.3624 (mtm180) REVERT: c 52 ILE cc_start: 0.8515 (pt) cc_final: 0.8247 (pt) REVERT: c 59 ILE cc_start: 0.9053 (mm) cc_final: 0.8750 (tt) REVERT: f 68 SER cc_start: 0.8445 (p) cc_final: 0.8052 (m) REVERT: b 29 SER cc_start: 0.8393 (m) cc_final: 0.7782 (t) REVERT: b 75 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8291 (tpp80) REVERT: b 119 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6075 (pp20) REVERT: a 19 ARG cc_start: 0.7039 (ptm-80) cc_final: 0.6242 (ptm-80) REVERT: a 223 TRP cc_start: 0.7751 (p-90) cc_final: 0.7471 (p-90) REVERT: h 8 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6848 (tp-100) REVERT: h 122 THR cc_start: 0.7271 (p) cc_final: 0.7056 (t) REVERT: h 136 ARG cc_start: 0.7798 (ttt-90) cc_final: 0.6554 (ttt-90) REVERT: g 104 ASP cc_start: 0.6900 (p0) cc_final: 0.6536 (p0) REVERT: g 106 ARG cc_start: 0.6601 (ttp-110) cc_final: 0.5706 (ttp80) REVERT: j 75 ARG cc_start: 0.7064 (ttt180) cc_final: 0.6377 (ptm160) REVERT: j 109 LEU cc_start: 0.8691 (tp) cc_final: 0.8488 (tt) REVERT: k 47 TYR cc_start: 0.6298 (m-10) cc_final: 0.6058 (m-10) REVERT: k 76 ARG cc_start: 0.7708 (tpt170) cc_final: 0.7391 (tpt170) outliers start: 27 outliers final: 20 residues processed: 385 average time/residue: 0.1512 time to fit residues: 83.5977 Evaluate side-chains 379 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 359 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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 264 THR Chi-restraints excluded: chain h residue 5 THR 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: 1.9990 chunk 198 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 284 GLN c 232 HIS g 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.222409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.181709 restraints weight = 23460.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.184815 restraints weight = 14477.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.187476 restraints weight = 10940.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.189043 restraints weight = 8621.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.189940 restraints weight = 7573.997| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16986 Z= 0.207 Angle : 0.980 20.313 23283 Z= 0.442 Chirality : 0.070 0.983 2766 Planarity : 0.007 0.076 2903 Dihedral : 12.650 179.973 2614 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Rotamer: Outliers : 4.39 % Allowed : 17.45 % Favored : 78.16 % 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: -2.36 (0.19), residues: 2005 helix: 0.70 (0.21), residues: 619 sheet: -1.25 (0.32), residues: 264 loop : -3.18 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 114 TYR 0.016 0.001 TYR j 47 PHE 0.013 0.002 PHE f 70 TRP 0.017 0.002 TRP f 281 HIS 0.007 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (16986) covalent geometry : angle 0.97993 / 0.44 (23283) hydrogen bonds : bond 0.04313 / 2.91 ( 548) hydrogen bonds : angle 5.21559 / 3.60 ( 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 425 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 352 time to evaluate : 0.592 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 120 ARG cc_start: 0.5352 (mtm180) cc_final: 0.3668 (mtm180) REVERT: c 52 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (pt) REVERT: c 59 ILE cc_start: 0.9122 (mm) cc_final: 0.8816 (tt) REVERT: f 68 SER cc_start: 0.8489 (p) cc_final: 0.8183 (m) REVERT: b 29 SER cc_start: 0.8449 (m) cc_final: 0.7859 (t) REVERT: b 232 HIS cc_start: 0.7799 (m-70) cc_final: 0.6944 (m-70) REVERT: b 254 SER cc_start: 0.8900 (p) cc_final: 0.8278 (t) REVERT: a 48 ARG cc_start: 0.6417 (tpt-90) cc_final: 0.5767 (tpt-90) REVERT: a 141 MET cc_start: 0.7538 (mmm) cc_final: 0.6945 (mmm) REVERT: h 8 GLN cc_start: 0.7312 (mm-40) cc_final: 0.6950 (tp40) REVERT: h 113 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (mt) REVERT: h 122 THR cc_start: 0.7573 (p) cc_final: 0.7275 (t) REVERT: g 104 ASP cc_start: 0.7115 (p0) cc_final: 0.6813 (p0) REVERT: g 106 ARG cc_start: 0.6714 (ttp-110) cc_final: 0.5676 (ttp80) REVERT: i 90 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8037 (tm-30) outliers start: 73 outliers final: 51 residues processed: 380 average time/residue: 0.1415 time to fit residues: 80.0217 Evaluate side-chains 386 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 333 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 77 VAL 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 52 ILE Chi-restraints excluded: chain c residue 129 ILE 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 f residue 29 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 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 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 211 ILE Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 266 THR Chi-restraints excluded: chain a residue 73 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 70 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 94 GLN Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 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 142 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 131 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 0.0770 chunk 142 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 232 HIS f 32 HIS b 32 HIS ** 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 = 0.4366 r_free = 0.4366 target = 0.231630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.191790 restraints weight = 23177.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.196072 restraints weight = 14696.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.197640 restraints weight = 10933.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.199569 restraints weight = 8920.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.201001 restraints weight = 7536.110| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16986 Z= 0.165 Angle : 0.899 13.434 23283 Z= 0.407 Chirality : 0.063 0.728 2766 Planarity : 0.006 0.072 2903 Dihedral : 12.085 176.102 2614 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Rotamer: Outliers : 4.27 % Allowed : 20.64 % Favored : 75.09 % 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: -2.24 (0.19), residues: 2005 helix: 0.93 (0.21), residues: 619 sheet: -1.17 (0.32), residues: 264 loop : -3.19 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG k 106 TYR 0.008 0.001 TYR i 47 PHE 0.011 0.001 PHE f 44 TRP 0.017 0.001 TRP c 281 HIS 0.005 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (16986) covalent geometry : angle 0.89917 / 0.41 (23283) hydrogen bonds : bond 0.03876 / 2.59 ( 548) hydrogen bonds : angle 5.03878 / 3.47 ( 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 412 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 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: symmetry clash revert: symmetry clash REVERT: d 120 ARG cc_start: 0.5323 (mtm180) cc_final: 0.3606 (mtm180) REVERT: c 52 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8331 (pt) REVERT: c 59 ILE cc_start: 0.9120 (mm) cc_final: 0.8796 (tt) REVERT: f 33 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7685 (mtt90) REVERT: f 68 SER cc_start: 0.8451 (p) cc_final: 0.8159 (m) REVERT: b 29 SER cc_start: 0.8449 (m) cc_final: 0.7861 (t) REVERT: b 91 VAL cc_start: 0.7863 (p) cc_final: 0.7644 (m) REVERT: b 231 GLU cc_start: 0.5688 (tm-30) cc_final: 0.5249 (tm-30) REVERT: b 232 HIS cc_start: 0.7579 (m-70) cc_final: 0.6758 (m-70) REVERT: b 254 SER cc_start: 0.8907 (p) cc_final: 0.8292 (t) REVERT: a 48 ARG cc_start: 0.6486 (tpt-90) cc_final: 0.5930 (tpt-90) REVERT: a 56 ASP cc_start: 0.6843 (m-30) cc_final: 0.6368 (p0) REVERT: a 141 MET cc_start: 0.7645 (mmm) cc_final: 0.7081 (mmm) REVERT: h 8 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6817 (mm-40) REVERT: h 33 ARG cc_start: 0.7722 (mpt180) cc_final: 0.7268 (mpt90) REVERT: h 122 THR cc_start: 0.7482 (p) cc_final: 0.7199 (t) REVERT: g 104 ASP cc_start: 0.6906 (p0) cc_final: 0.6667 (p0) REVERT: g 106 ARG cc_start: 0.6798 (ttp-110) cc_final: 0.5901 (ttt90) REVERT: i 90 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8174 (tm-30) outliers start: 71 outliers final: 51 residues processed: 371 average time/residue: 0.1432 time to fit residues: 77.8998 Evaluate side-chains 381 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 328 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 140 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 46 LEU 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 221 GLN Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 266 THR 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 52 ILE Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG 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 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 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 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain g residue 112 LEU 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 142 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 113 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 144 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 61 GLN c 232 HIS a 32 HIS h 94 GLN ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.225900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.185748 restraints weight = 23183.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.189725 restraints weight = 14656.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.191706 restraints weight = 11024.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.193624 restraints weight = 8798.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.194495 restraints weight = 7443.318| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16986 Z= 0.142 Angle : 0.850 12.316 23283 Z= 0.384 Chirality : 0.057 0.533 2766 Planarity : 0.005 0.060 2903 Dihedral : 11.932 176.216 2614 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 4.63 % Allowed : 22.02 % Favored : 73.35 % 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: -2.12 (0.19), residues: 2005 helix: 1.01 (0.21), residues: 624 sheet: -1.04 (0.32), residues: 264 loop : -3.14 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 40 TYR 0.010 0.001 TYR j 47 PHE 0.012 0.001 PHE c 70 TRP 0.016 0.001 TRP c 281 HIS 0.006 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16986) covalent geometry : angle 0.85030 / 0.38 (23283) hydrogen bonds : bond 0.03574 / 2.39 ( 548) hydrogen bonds : angle 4.86526 / 3.34 ( 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 409 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 332 time to evaluate : 0.548 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: 0.8548 (Cg_endo) cc_final: 0.8295 (Cg_exo) REVERT: e 226 LEU cc_start: 0.8149 (mt) cc_final: 0.7829 (mt) REVERT: e 285 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6251 (tp) REVERT: d 118 GLU cc_start: 0.6592 (mm-30) cc_final: 0.5314 (pm20) REVERT: d 120 ARG cc_start: 0.5429 (mtm180) cc_final: 0.3897 (mtm180) REVERT: d 141 MET cc_start: 0.8133 (mmp) cc_final: 0.7913 (tpp) REVERT: c 52 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8258 (pt) REVERT: f 33 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (mtt90) REVERT: b 29 SER cc_start: 0.8518 (m) cc_final: 0.7895 (t) REVERT: b 232 HIS cc_start: 0.7681 (m-70) cc_final: 0.7436 (m-70) REVERT: b 254 SER cc_start: 0.8869 (p) cc_final: 0.8292 (t) REVERT: a 48 ARG cc_start: 0.6592 (tpt-90) cc_final: 0.5880 (tpt-90) REVERT: a 56 ASP cc_start: 0.6939 (m-30) cc_final: 0.6483 (p0) REVERT: a 141 MET cc_start: 0.7755 (mmm) cc_final: 0.7192 (mmm) REVERT: h 33 ARG cc_start: 0.7700 (mpt180) cc_final: 0.7236 (mpt90) REVERT: h 122 THR cc_start: 0.7452 (p) cc_final: 0.7217 (t) REVERT: g 94 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7682 (tm-30) REVERT: g 104 ASP cc_start: 0.6973 (p0) cc_final: 0.6735 (p0) REVERT: g 106 ARG cc_start: 0.6687 (ttp-110) cc_final: 0.5867 (ttp-170) REVERT: k 40 ARG cc_start: 0.7361 (ttm170) cc_final: 0.6948 (ttm-80) REVERT: k 47 TYR cc_start: 0.6215 (m-10) cc_final: 0.5961 (m-10) outliers start: 77 outliers final: 55 residues processed: 376 average time/residue: 0.1469 time to fit residues: 81.2157 Evaluate side-chains 383 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 325 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 81 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 266 THR 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 52 ILE 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 242 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 177 VAL 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 168 THR Chi-restraints excluded: chain h residue 42 LEU 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 31 THR Chi-restraints excluded: chain g residue 112 LEU 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 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 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 58 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 112 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 32 HIS f 260 GLN ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.210873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.170268 restraints weight = 23358.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.171599 restraints weight = 15693.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.174145 restraints weight = 12720.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.175415 restraints weight = 10182.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.178040 restraints weight = 8624.627| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 16986 Z= 0.309 Angle : 1.050 15.170 23283 Z= 0.488 Chirality : 0.067 0.745 2766 Planarity : 0.008 0.146 2903 Dihedral : 12.379 175.812 2614 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 17.11 % Favored : 82.79 % Rotamer: Outliers : 6.14 % Allowed : 22.20 % Favored : 71.66 % 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: -2.47 (0.18), residues: 2005 helix: 0.70 (0.21), residues: 619 sheet: -1.10 (0.32), residues: 264 loop : -3.36 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG d 139 TYR 0.013 0.002 TYR d 88 PHE 0.017 0.002 PHE e 237 TRP 0.019 0.002 TRP g 10 HIS 0.008 0.002 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.31 (16986) covalent geometry : angle 1.05034 / 0.49 (23283) hydrogen bonds : bond 0.04994 / 3.38 ( 548) hydrogen bonds : angle 5.35655 / 3.68 ( 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 441 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 339 time to evaluate : 0.581 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: 0.8685 (Cg_endo) cc_final: 0.8410 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7376 (m-10) cc_final: 0.7137 (m-10) REVERT: d 118 GLU cc_start: 0.5587 (mm-30) cc_final: 0.4486 (pm20) REVERT: d 120 ARG cc_start: 0.4996 (mtm180) cc_final: 0.3029 (mtm180) REVERT: d 128 GLN cc_start: 0.9063 (tp-100) cc_final: 0.8839 (tp-100) REVERT: c 52 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8416 (pt) REVERT: c 59 ILE cc_start: 0.9104 (mm) cc_final: 0.8858 (tt) REVERT: f 33 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7766 (mtt90) REVERT: f 232 HIS cc_start: 0.7019 (m-70) cc_final: 0.6514 (m90) REVERT: b 29 SER cc_start: 0.8492 (m) cc_final: 0.7903 (t) REVERT: b 91 VAL cc_start: 0.7928 (p) cc_final: 0.7687 (m) REVERT: b 232 HIS cc_start: 0.7599 (m-70) cc_final: 0.7362 (m90) REVERT: b 254 SER cc_start: 0.8983 (p) cc_final: 0.8420 (t) REVERT: a 48 ARG cc_start: 0.6823 (tpt-90) cc_final: 0.6112 (tpt-90) REVERT: a 56 ASP cc_start: 0.7039 (m-30) cc_final: 0.6519 (p0) REVERT: a 126 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6942 (tt) REVERT: a 141 MET cc_start: 0.7799 (mmm) cc_final: 0.7245 (mmm) REVERT: h 33 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7249 (mpt90) REVERT: h 122 THR cc_start: 0.7678 (p) cc_final: 0.7416 (t) REVERT: g 94 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7705 (tm-30) REVERT: g 106 ARG cc_start: 0.6667 (ttp-110) cc_final: 0.5848 (ttp-170) REVERT: g 118 LEU cc_start: 0.8518 (tp) cc_final: 0.8239 (tp) REVERT: g 132 LEU cc_start: 0.8145 (mm) cc_final: 0.7710 (mm) REVERT: k 40 ARG cc_start: 0.7407 (ttm170) cc_final: 0.6908 (ttm-80) REVERT: k 70 LEU cc_start: 0.8741 (tp) cc_final: 0.8533 (tp) outliers start: 102 outliers final: 79 residues processed: 400 average time/residue: 0.1348 time to fit residues: 80.5136 Evaluate side-chains 418 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 336 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 140 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 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 148 SER Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 227 ASP 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 52 ILE 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 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 171 LEU Chi-restraints excluded: chain f residue 177 VAL Chi-restraints excluded: chain f residue 254 SER Chi-restraints excluded: chain f residue 265 VAL 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 211 ILE 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 73 VAL Chi-restraints excluded: chain a residue 126 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 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 133 LEU Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.218253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.177735 restraints weight = 23153.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.180257 restraints weight = 14924.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.183047 restraints weight = 11342.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.185097 restraints weight = 8724.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.186053 restraints weight = 7545.461| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4192 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= 0.162 Angle : 0.905 13.438 23283 Z= 0.412 Chirality : 0.058 0.560 2766 Planarity : 0.006 0.060 2903 Dihedral : 12.072 174.328 2614 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.41 % Favored : 85.59 % Rotamer: Outliers : 4.99 % Allowed : 24.49 % Favored : 70.52 % 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: -2.26 (0.19), residues: 2005 helix: 0.87 (0.21), residues: 630 sheet: -0.97 (0.32), residues: 264 loop : -3.28 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG d 139 TYR 0.010 0.001 TYR h 47 PHE 0.008 0.001 PHE b 70 TRP 0.021 0.001 TRP c 281 HIS 0.007 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16986) covalent geometry : angle 0.90488 / 0.41 (23283) hydrogen bonds : bond 0.03941 / 2.64 ( 548) hydrogen bonds : angle 5.07138 / 3.47 ( 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 417 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 334 time to evaluate : 0.652 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 33 ARG cc_start: 0.7725 (tpp80) cc_final: 0.7475 (tpp80) REVERT: e 127 PRO cc_start: 0.8668 (Cg_endo) cc_final: 0.8397 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7241 (m-10) cc_final: 0.7027 (m-10) REVERT: d 118 GLU cc_start: 0.5488 (mm-30) cc_final: 0.3353 (pm20) REVERT: d 120 ARG cc_start: 0.4811 (mtm180) cc_final: 0.2622 (mtm180) REVERT: d 128 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8910 (tp-100) REVERT: d 285 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5644 (tp) REVERT: c 59 ILE cc_start: 0.9080 (mm) cc_final: 0.8809 (tt) REVERT: b 29 SER cc_start: 0.8488 (m) cc_final: 0.7866 (t) REVERT: b 86 LEU cc_start: 0.7299 (mt) cc_final: 0.7095 (mt) REVERT: b 91 VAL cc_start: 0.7885 (p) cc_final: 0.7656 (m) REVERT: b 232 HIS cc_start: 0.7606 (m-70) cc_final: 0.7393 (m90) REVERT: a 46 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6219 (pt) REVERT: a 48 ARG cc_start: 0.6738 (tpt-90) cc_final: 0.5978 (tpt-90) REVERT: a 56 ASP cc_start: 0.6952 (m-30) cc_final: 0.6500 (p0) REVERT: a 126 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6792 (tt) REVERT: a 141 MET cc_start: 0.7779 (mmm) cc_final: 0.7249 (mmm) REVERT: h 33 ARG cc_start: 0.7855 (mpt180) cc_final: 0.7245 (mpt180) REVERT: h 122 THR cc_start: 0.7524 (p) cc_final: 0.7255 (t) REVERT: g 73 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7832 (mmm-85) REVERT: g 94 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7658 (tm-30) REVERT: g 106 ARG cc_start: 0.6478 (ttp-110) cc_final: 0.5664 (ttp-170) REVERT: g 118 LEU cc_start: 0.8503 (tp) cc_final: 0.8160 (tp) REVERT: j 114 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7657 (ttm110) REVERT: i 11 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6965 (mtt180) outliers start: 83 outliers final: 60 residues processed: 378 average time/residue: 0.1365 time to fit residues: 76.2921 Evaluate side-chains 385 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE 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 227 ASP Chi-restraints excluded: chain d residue 266 THR 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 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 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 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 177 VAL 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 241 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 126 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 g residue 29 SER 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 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 114 ARG 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 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 58 ASP 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: 2.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.219226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.178744 restraints weight = 23256.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.181329 restraints weight = 15118.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.183956 restraints weight = 11529.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.186609 restraints weight = 8721.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.186982 restraints weight = 7432.157| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16986 Z= 0.155 Angle : 0.878 13.145 23283 Z= 0.399 Chirality : 0.056 0.539 2766 Planarity : 0.006 0.063 2903 Dihedral : 11.938 175.647 2614 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.21 % Favored : 84.79 % Rotamer: Outliers : 4.57 % Allowed : 25.45 % Favored : 69.98 % 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: -2.14 (0.19), residues: 2005 helix: 0.99 (0.21), residues: 624 sheet: -0.90 (0.32), residues: 264 loop : -3.20 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG i 75 TYR 0.011 0.001 TYR j 47 PHE 0.019 0.001 PHE f 236 TRP 0.032 0.001 TRP g 87 HIS 0.006 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16986) covalent geometry : angle 0.87844 / 0.40 (23283) hydrogen bonds : bond 0.03765 / 2.52 ( 548) hydrogen bonds : angle 4.97133 / 3.40 ( 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 406 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 330 time to evaluate : 0.592 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: 0.8713 (Cg_endo) cc_final: 0.8452 (Cg_exo) REVERT: d 117 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4830 (mt-10) REVERT: d 118 GLU cc_start: 0.5199 (mm-30) cc_final: 0.4329 (pm20) REVERT: d 120 ARG cc_start: 0.5256 (mtm180) cc_final: 0.2812 (mtm180) REVERT: d 128 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8885 (tp-100) REVERT: c 52 ILE cc_start: 0.8610 (pt) cc_final: 0.8313 (mp) REVERT: f 68 SER cc_start: 0.8450 (p) cc_final: 0.8243 (m) REVERT: f 232 HIS cc_start: 0.6861 (m-70) cc_final: 0.6209 (m-70) REVERT: f 266 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6780 (p) REVERT: b 29 SER cc_start: 0.8586 (m) cc_final: 0.7944 (t) REVERT: b 232 HIS cc_start: 0.7600 (m-70) cc_final: 0.7387 (m90) REVERT: b 254 SER cc_start: 0.8901 (p) cc_final: 0.8372 (t) REVERT: a 48 ARG cc_start: 0.6713 (tpt-90) cc_final: 0.5976 (tpt-90) REVERT: a 56 ASP cc_start: 0.6947 (m-30) cc_final: 0.6522 (p0) REVERT: a 126 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6820 (tt) REVERT: a 141 MET cc_start: 0.7706 (mmm) cc_final: 0.7169 (mmm) REVERT: h 33 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7257 (mpt180) REVERT: h 122 THR cc_start: 0.7585 (p) cc_final: 0.7340 (t) REVERT: g 94 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7639 (tm-30) REVERT: g 106 ARG cc_start: 0.6537 (ttp-110) cc_final: 0.5791 (ttp-170) REVERT: g 118 LEU cc_start: 0.8471 (tp) cc_final: 0.8175 (tp) REVERT: j 114 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7491 (ttm110) REVERT: k 40 ARG cc_start: 0.7306 (ttm170) cc_final: 0.6816 (ttt180) outliers start: 76 outliers final: 61 residues processed: 372 average time/residue: 0.1405 time to fit residues: 77.8939 Evaluate side-chains 388 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 323 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 117 GLU 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 227 ASP Chi-restraints excluded: chain d residue 266 THR 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 141 MET Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 175 LEU 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 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 177 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 145 LEU Chi-restraints excluded: chain b residue 241 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 126 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 g residue 29 SER 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 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 114 ARG 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 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 58 ASP Chi-restraints excluded: chain i residue 83 THR 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: 0.2980 chunk 137 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 140 optimal weight: 0.0040 chunk 172 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 159 HIS e 247 HIS k 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.231484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.193882 restraints weight = 23046.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.196259 restraints weight = 15164.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.197790 restraints weight = 10719.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.199121 restraints weight = 9440.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.199420 restraints weight = 8213.643| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16986 Z= 0.139 Angle : 0.853 12.300 23283 Z= 0.388 Chirality : 0.053 0.493 2766 Planarity : 0.006 0.097 2903 Dihedral : 11.728 174.939 2614 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 4.03 % Allowed : 26.05 % Favored : 69.92 % 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: -2.01 (0.19), residues: 2005 helix: 1.10 (0.21), residues: 624 sheet: -0.83 (0.32), residues: 264 loop : -3.11 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 75 TYR 0.007 0.001 TYR h 47 PHE 0.015 0.001 PHE c 70 TRP 0.026 0.001 TRP g 87 HIS 0.005 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16986) covalent geometry : angle 0.85333 / 0.39 (23283) hydrogen bonds : bond 0.03421 / 2.27 ( 548) hydrogen bonds : angle 4.80343 / 3.28 ( 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 410 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 343 time to evaluate : 0.634 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: 0.8649 (Cg_endo) cc_final: 0.8396 (Cg_exo) REVERT: d 118 GLU cc_start: 0.5316 (mm-30) cc_final: 0.4935 (pm20) REVERT: d 120 ARG cc_start: 0.5301 (mtm180) cc_final: 0.3001 (mtm180) REVERT: d 128 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8841 (tp-100) REVERT: f 33 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7449 (mtt90) REVERT: f 232 HIS cc_start: 0.6867 (m-70) cc_final: 0.6221 (m-70) REVERT: f 266 THR cc_start: 0.6995 (OUTLIER) cc_final: 0.6771 (p) REVERT: b 29 SER cc_start: 0.8622 (m) cc_final: 0.7997 (t) REVERT: b 79 GLU cc_start: 0.7360 (tt0) cc_final: 0.7084 (tt0) REVERT: b 232 HIS cc_start: 0.7666 (m-70) cc_final: 0.7438 (m90) REVERT: b 254 SER cc_start: 0.8959 (p) cc_final: 0.8500 (t) REVERT: a 48 ARG cc_start: 0.6646 (tpt-90) cc_final: 0.5957 (tpt-90) REVERT: a 56 ASP cc_start: 0.6959 (m-30) cc_final: 0.6460 (p0) REVERT: a 141 MET cc_start: 0.7571 (mmm) cc_final: 0.7102 (mmm) REVERT: a 284 GLN cc_start: 0.6064 (pp30) cc_final: 0.4916 (mp10) REVERT: h 33 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7228 (mpt180) REVERT: h 122 THR cc_start: 0.7445 (p) cc_final: 0.7234 (t) REVERT: g 94 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7736 (tm-30) REVERT: g 106 ARG cc_start: 0.6437 (ttp-110) cc_final: 0.5759 (ttp-170) REVERT: g 118 LEU cc_start: 0.8464 (tp) cc_final: 0.8190 (tp) REVERT: k 40 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6849 (ttt180) REVERT: k 128 LEU cc_start: 0.8863 (tp) cc_final: 0.8524 (mm) REVERT: i 133 LEU cc_start: 0.8578 (tp) cc_final: 0.8355 (tp) outliers start: 67 outliers final: 56 residues processed: 375 average time/residue: 0.1394 time to fit residues: 77.8591 Evaluate side-chains 383 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 264 THR Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 266 THR 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 167 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU 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 167 SER Chi-restraints excluded: chain f residue 177 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 145 LEU Chi-restraints excluded: chain b residue 241 LEU Chi-restraints excluded: chain b residue 264 THR 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 g residue 29 SER 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 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 114 ARG 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 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain i residue 58 ASP 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 13 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 172 optimal weight: 0.0270 chunk 76 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.231364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.193433 restraints weight = 22919.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.195784 restraints weight = 15255.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.198221 restraints weight = 11218.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.199316 restraints weight = 9536.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.199588 restraints weight = 8009.133| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16986 Z= 0.139 Angle : 0.856 13.091 23283 Z= 0.388 Chirality : 0.053 0.487 2766 Planarity : 0.006 0.079 2903 Dihedral : 11.645 176.009 2614 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.56 % Favored : 85.44 % Rotamer: Outliers : 3.43 % Allowed : 26.77 % Favored : 69.80 % 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: -1.95 (0.19), residues: 2005 helix: 1.11 (0.21), residues: 624 sheet: -0.78 (0.31), residues: 264 loop : -3.05 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 219 TYR 0.010 0.001 TYR j 47 PHE 0.017 0.001 PHE c 70 TRP 0.027 0.001 TRP g 87 HIS 0.004 0.001 HIS f 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16986) covalent geometry : angle 0.85636 / 0.39 (23283) hydrogen bonds : bond 0.03462 / 2.29 ( 548) hydrogen bonds : angle 4.76341 / 3.26 ( 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 373 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.595 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: 0.8709 (Cg_endo) cc_final: 0.8457 (Cg_exo) REVERT: d 117 GLU cc_start: 0.5087 (OUTLIER) cc_final: 0.4803 (mt-10) REVERT: d 120 ARG cc_start: 0.5288 (mtm180) cc_final: 0.2931 (mtm180) REVERT: d 128 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8849 (tp-100) REVERT: f 33 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7439 (mtt90) REVERT: f 233 GLN cc_start: 0.8526 (mp10) cc_final: 0.8291 (pm20) REVERT: f 266 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6857 (p) REVERT: b 29 SER cc_start: 0.8625 (m) cc_final: 0.8005 (t) REVERT: b 79 GLU cc_start: 0.7384 (tt0) cc_final: 0.7154 (tt0) REVERT: b 232 HIS cc_start: 0.7636 (m-70) cc_final: 0.7401 (m90) REVERT: b 254 SER cc_start: 0.8960 (p) cc_final: 0.8498 (t) REVERT: a 48 ARG cc_start: 0.6650 (tpt-90) cc_final: 0.5927 (tpt-90) REVERT: a 56 ASP cc_start: 0.6995 (m-30) cc_final: 0.6498 (p0) REVERT: a 126 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6739 (tt) REVERT: a 141 MET cc_start: 0.7584 (mmm) cc_final: 0.7109 (mmm) REVERT: h 33 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7245 (mpt180) REVERT: h 122 THR cc_start: 0.7523 (p) cc_final: 0.7270 (t) REVERT: g 94 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7804 (tm-30) REVERT: g 106 ARG cc_start: 0.6472 (ttp-110) cc_final: 0.5797 (ttp-170) REVERT: g 118 LEU cc_start: 0.8540 (tp) cc_final: 0.8250 (tp) REVERT: k 40 ARG cc_start: 0.7268 (ttm170) cc_final: 0.6804 (ttt180) REVERT: i 114 ARG cc_start: 0.6200 (ptt90) cc_final: 0.5929 (ptt-90) REVERT: i 133 LEU cc_start: 0.8596 (tp) cc_final: 0.8357 (tp) outliers start: 57 outliers final: 53 residues processed: 348 average time/residue: 0.1370 time to fit residues: 71.1164 Evaluate side-chains 370 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 264 THR Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 117 GLU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 266 THR 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 168 THR Chi-restraints excluded: chain c residue 175 LEU Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 177 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 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 168 THR Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h 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 83 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 114 ARG 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 112 LEU Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain i residue 58 ASP 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: 10.0000 chunk 114 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 128 GLN g 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.217477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.179437 restraints weight = 22453.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.181699 restraints weight = 14767.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.184105 restraints weight = 10771.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.186500 restraints weight = 8613.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.188058 restraints weight = 6824.384| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16986 Z= 0.159 Angle : 0.874 12.867 23283 Z= 0.397 Chirality : 0.054 0.523 2766 Planarity : 0.006 0.079 2903 Dihedral : 11.731 176.391 2614 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 3.91 % Allowed : 26.53 % Favored : 69.55 % 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: -1.93 (0.19), residues: 2005 helix: 1.11 (0.21), residues: 624 sheet: -0.71 (0.32), residues: 264 loop : -3.04 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 76 TYR 0.010 0.001 TYR j 47 PHE 0.015 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/Z covalent geometry : bond 0.00363 / 0.16 (16986) covalent geometry : angle 0.87421 / 0.40 (23283) hydrogen bonds : bond 0.03642 / 2.43 ( 548) hydrogen bonds : angle 4.83518 / 3.31 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.93 seconds wall clock time: 51 minutes 16.01 seconds (3076.01 seconds total)