Starting phenix.real_space_refine on Fri Jul 3 08:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9h_41111/07_2026/8t9h_41111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9h_41111/07_2026/8t9h_41111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2026/8t9h_41111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2026/8t9h_41111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2026/8t9h_41111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2026/8t9h_41111.map" } resolution = 3.37 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= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic. 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 201 5.49 5 S 29 5.16 5 C 6930 2.51 5 N 2237 2.21 5 O 2642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2012 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "J" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2110 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "K" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1969 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12039 At special positions: 0 Unit cell: (92.064, 118.368, 127.136, 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 29 16.00 P 201 15.00 O 2642 8.00 N 2237 7.00 C 6930 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: 0.76 Conformation dependent library (CDL) restraints added in 364.6 milliseconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 65.9% alpha, 5.5% beta 96 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.990A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.523A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.569A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.511A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.505A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.173A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.669A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.492A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 39 through 50 removed outlier: 3.524A pdb=" N TYR H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.609A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 134 through 148 removed outlier: 3.697A pdb=" N LYS K 138 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.652A pdb=" N LEU K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN K 169 " --> pdb=" O HIS K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 188 removed outlier: 3.509A pdb=" N ILE K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 243 removed outlier: 3.709A pdb=" N ASN K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K 241 " --> pdb=" O ILE K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.683A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 328 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 354 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.154A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 removed outlier: 3.570A pdb=" N CYS K 260 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA K 232 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU K 265 " --> pdb=" O CYS K 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.652A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.453A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.049A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.287A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 195 through 199 removed outlier: 3.697A pdb=" N GLU K 301 " --> pdb=" O ALA K 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 279 through 283 483 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 247 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2831 1.33 - 1.45: 3313 1.45 - 1.57: 6062 1.57 - 1.69: 400 1.69 - 1.81: 44 Bond restraints: 12650 Sorted by residual: bond pdb=" C5' DA I 49 " pdb=" C4' DA I 49 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.94e+00 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.20e+00 bond pdb=" C3' DA J 44 " pdb=" C2' DA J 44 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 bond pdb=" C3' DG I 94 " pdb=" C2' DG I 94 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.78e+00 ... (remaining 12645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 16396 1.11 - 2.23: 1208 2.23 - 3.34: 289 3.34 - 4.46: 26 4.46 - 5.57: 9 Bond angle restraints: 17928 Sorted by residual: angle pdb=" O4' DA I 49 " pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " ideal model delta sigma weight residual 106.00 102.23 3.77 6.00e-01 2.78e+00 3.95e+01 angle pdb=" O4' DG I 100 " pdb=" C4' DG I 100 " pdb=" C3' DG I 100 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.70e+01 angle pdb=" O4' DA I 39 " pdb=" C4' DA I 39 " pdb=" C3' DA I 39 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O4' DG I 34 " pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " pdb=" C2' DA I 49 " ideal model delta sigma weight residual 103.10 98.93 4.17 9.00e-01 1.23e+00 2.15e+01 ... (remaining 17923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 6152 35.17 - 70.34: 927 70.34 - 105.50: 42 105.50 - 140.67: 0 140.67 - 175.84: 3 Dihedral angle restraints: 7124 sinusoidal: 4214 harmonic: 2910 Sorted by residual: dihedral pdb=" C4' DA J 44 " pdb=" C3' DA J 44 " pdb=" O3' DA J 44 " pdb=" P DT J 45 " ideal model delta sinusoidal sigma weight residual 220.00 44.16 175.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 94 " pdb=" C3' DG I 94 " pdb=" O3' DG I 94 " pdb=" P DC I 95 " ideal model delta sinusoidal sigma weight residual 220.00 51.01 168.99 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 85 " pdb=" C3' DG I 85 " pdb=" O3' DG I 85 " pdb=" P DT I 86 " ideal model delta sinusoidal sigma weight residual 220.00 55.01 164.99 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1336 0.032 - 0.064: 472 0.064 - 0.097: 164 0.097 - 0.129: 54 0.129 - 0.161: 5 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C3' DG I 85 " pdb=" C4' DG I 85 " pdb=" O3' DG I 85 " pdb=" C2' DG I 85 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" P DT I 86 " pdb=" OP1 DT I 86 " pdb=" OP2 DT I 86 " pdb=" O5' DT I 86 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" C3' DA J 44 " pdb=" C4' DA J 44 " pdb=" O3' DA J 44 " pdb=" C2' DA J 44 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 2028 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 49 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.22e+00 pdb=" N9 DA I 49 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 49 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 49 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 49 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 49 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 49 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 49 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 98 " 0.001 2.00e-02 2.50e+03 1.40e-02 4.44e+00 pdb=" N1 DC J 98 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DC J 98 " -0.034 2.00e-02 2.50e+03 pdb=" O2 DC J 98 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DC J 98 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 98 " -0.013 2.00e-02 2.50e+03 pdb=" N4 DC J 98 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC J 98 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " -0.024 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 88 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.004 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2498 2.78 - 3.31: 11748 3.31 - 3.84: 23449 3.84 - 4.37: 25860 4.37 - 4.90: 39469 Nonbonded interactions: 103024 Sorted by model distance: nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.255 3.040 nonbonded pdb=" NE2 GLN K 262 " pdb=" O LEU K 263 " model vdw 2.256 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.256 3.040 nonbonded pdb=" O GLU K 236 " pdb=" ND2 ASN K 240 " model vdw 2.264 3.120 nonbonded pdb=" O ILE K 271 " pdb=" OH TYR K 307 " model vdw 2.264 3.040 ... (remaining 103019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 125) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 0.037 12650 Z= 0.427 Angle : 0.657 5.574 17928 Z= 0.603 Chirality : 0.039 0.161 2031 Planarity : 0.004 0.034 1592 Dihedral : 24.898 175.838 5244 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 6.18 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.27), residues: 981 helix: 2.29 (0.21), residues: 624 sheet: -0.80 (0.82), residues: 44 loop : -0.37 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.008 0.001 TYR G 57 PHE 0.008 0.001 PHE E 78 TRP 0.004 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.43 (12650) covalent geometry : angle 0.65690 / 0.60 (17928) hydrogen bonds : bond 0.11301 / 7.55 ( 730) hydrogen bonds : angle 4.85681 / 3.44 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8624 (tp-100) REVERT: C 90 ASP cc_start: 0.8267 (t70) cc_final: 0.7652 (t0) REVERT: C 92 GLU cc_start: 0.8607 (mp0) cc_final: 0.7966 (mp0) REVERT: C 104 GLN cc_start: 0.8060 (mp10) cc_final: 0.7564 (mp10) REVERT: D 51 ASP cc_start: 0.8292 (p0) cc_final: 0.7962 (p0) REVERT: D 68 ASP cc_start: 0.8875 (t70) cc_final: 0.8551 (t0) REVERT: D 93 GLU cc_start: 0.8430 (mp0) cc_final: 0.7859 (mp0) REVERT: D 123 SER cc_start: 0.7785 (m) cc_final: 0.7510 (p) REVERT: G 92 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8398 (mm-30) REVERT: K 185 TYR cc_start: 0.9105 (m-80) cc_final: 0.8396 (m-80) outliers start: 8 outliers final: 2 residues processed: 202 average time/residue: 0.0991 time to fit residues: 29.4646 Evaluate side-chains 173 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain G residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 40.0000 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 112 GLN G 112 GLN H 50 HIS K 134 GLN K 174 GLN K 240 ASN K 262 GLN K 346 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.068797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.045911 restraints weight = 56092.480| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.36 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12650 Z= 0.157 Angle : 0.607 6.672 17928 Z= 0.356 Chirality : 0.044 0.242 2031 Planarity : 0.004 0.042 1592 Dihedral : 29.783 178.297 3315 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 12.24 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.26), residues: 981 helix: 2.31 (0.20), residues: 634 sheet: -0.80 (0.82), residues: 44 loop : -0.45 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.021 0.001 TYR H 84 PHE 0.007 0.001 PHE E 78 TRP 0.021 0.003 TRP K 264 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (12650) covalent geometry : angle 0.60668 / 0.36 (17928) hydrogen bonds : bond 0.04702 / 3.18 ( 730) hydrogen bonds : angle 3.85474 / 2.76 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8540 (mtpt) REVERT: B 93 GLN cc_start: 0.8685 (mp10) cc_final: 0.8366 (mm-40) REVERT: C 90 ASP cc_start: 0.8075 (t70) cc_final: 0.7473 (t70) REVERT: C 92 GLU cc_start: 0.8831 (mp0) cc_final: 0.8388 (mp0) REVERT: C 104 GLN cc_start: 0.8128 (mp10) cc_final: 0.7567 (mp10) REVERT: D 51 ASP cc_start: 0.8959 (p0) cc_final: 0.8154 (p0) REVERT: D 68 ASP cc_start: 0.9178 (t70) cc_final: 0.8854 (t0) REVERT: D 93 GLU cc_start: 0.8886 (mp0) cc_final: 0.8075 (mp0) REVERT: D 123 SER cc_start: 0.8490 (m) cc_final: 0.8082 (p) REVERT: E 50 GLU cc_start: 0.9588 (tt0) cc_final: 0.9330 (tt0) REVERT: E 76 GLN cc_start: 0.8895 (tp40) cc_final: 0.8691 (tp40) REVERT: E 125 GLN cc_start: 0.9158 (pt0) cc_final: 0.8658 (pm20) REVERT: F 44 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8675 (mmtp) REVERT: G 90 ASP cc_start: 0.8737 (t0) cc_final: 0.8338 (t0) REVERT: G 92 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8491 (mm-30) REVERT: H 69 ASP cc_start: 0.9363 (t70) cc_final: 0.8918 (t0) REVERT: K 185 TYR cc_start: 0.9083 (m-80) cc_final: 0.8399 (m-80) outliers start: 10 outliers final: 7 residues processed: 187 average time/residue: 0.1020 time to fit residues: 27.9299 Evaluate side-chains 181 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.067160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044257 restraints weight = 57170.619| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.36 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12650 Z= 0.236 Angle : 0.640 7.165 17928 Z= 0.368 Chirality : 0.045 0.257 2031 Planarity : 0.004 0.042 1592 Dihedral : 29.952 177.535 3314 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 11.88 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.27), residues: 981 helix: 2.32 (0.20), residues: 637 sheet: -0.92 (0.79), residues: 44 loop : -0.51 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.018 0.002 TYR D 37 PHE 0.008 0.001 PHE A 78 TRP 0.005 0.001 TRP K 218 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 (12650) covalent geometry : angle 0.64013 / 0.37 (17928) hydrogen bonds : bond 0.05253 / 3.54 ( 730) hydrogen bonds : angle 3.77300 / 2.71 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8469 (tp-100) REVERT: A 133 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 44 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8616 (mtpt) REVERT: B 84 MET cc_start: 0.8673 (mmm) cc_final: 0.8423 (tpp) REVERT: C 90 ASP cc_start: 0.8171 (t70) cc_final: 0.7600 (t70) REVERT: C 92 GLU cc_start: 0.8836 (mp0) cc_final: 0.8351 (mp0) REVERT: C 104 GLN cc_start: 0.8204 (mp10) cc_final: 0.7537 (mp10) REVERT: D 51 ASP cc_start: 0.9061 (p0) cc_final: 0.8374 (p0) REVERT: D 68 ASP cc_start: 0.9247 (t70) cc_final: 0.8899 (t0) REVERT: D 93 GLU cc_start: 0.8924 (mp0) cc_final: 0.8069 (mp0) REVERT: D 123 SER cc_start: 0.8424 (m) cc_final: 0.7936 (p) REVERT: E 50 GLU cc_start: 0.9574 (tt0) cc_final: 0.9361 (tt0) REVERT: E 80 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9280 (m) REVERT: E 81 ASP cc_start: 0.9320 (p0) cc_final: 0.9035 (p0) REVERT: E 125 GLN cc_start: 0.9221 (pt0) cc_final: 0.8976 (pt0) REVERT: F 44 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8663 (mmtp) REVERT: G 90 ASP cc_start: 0.8751 (t0) cc_final: 0.8401 (t0) REVERT: K 185 TYR cc_start: 0.8920 (m-80) cc_final: 0.8299 (m-80) outliers start: 16 outliers final: 10 residues processed: 173 average time/residue: 0.1012 time to fit residues: 25.6692 Evaluate side-chains 173 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 7 optimal weight: 0.0770 chunk 91 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.067570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044682 restraints weight = 56663.526| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.36 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12650 Z= 0.185 Angle : 0.612 7.182 17928 Z= 0.352 Chirality : 0.045 0.267 2031 Planarity : 0.004 0.038 1592 Dihedral : 29.990 178.405 3313 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.94 % Allowed : 12.12 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 981 helix: 2.33 (0.20), residues: 635 sheet: -0.98 (0.78), residues: 44 loop : -0.55 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 80 TYR 0.014 0.001 TYR H 41 PHE 0.007 0.001 PHE D 70 TRP 0.005 0.001 TRP K 218 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (12650) covalent geometry : angle 0.61181 / 0.35 (17928) hydrogen bonds : bond 0.04585 / 3.10 ( 730) hydrogen bonds : angle 3.65322 / 2.62 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.320 Fit side-chains REVERT: A 76 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8404 (tp-100) REVERT: B 44 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8556 (mtpt) REVERT: B 84 MET cc_start: 0.8670 (mmm) cc_final: 0.8146 (tpp) REVERT: C 90 ASP cc_start: 0.8174 (t70) cc_final: 0.7640 (t0) REVERT: C 92 GLU cc_start: 0.8849 (mp0) cc_final: 0.8323 (mp0) REVERT: C 104 GLN cc_start: 0.8260 (mp10) cc_final: 0.7541 (mp10) REVERT: D 51 ASP cc_start: 0.9029 (p0) cc_final: 0.8329 (p0) REVERT: D 62 MET cc_start: 0.9293 (tpp) cc_final: 0.9081 (mmp) REVERT: D 68 ASP cc_start: 0.9221 (t70) cc_final: 0.8936 (t0) REVERT: D 93 GLU cc_start: 0.8925 (mp0) cc_final: 0.8048 (mp0) REVERT: D 123 SER cc_start: 0.8413 (m) cc_final: 0.7996 (p) REVERT: E 50 GLU cc_start: 0.9556 (tt0) cc_final: 0.9337 (tt0) REVERT: E 125 GLN cc_start: 0.9206 (pt0) cc_final: 0.8905 (pt0) REVERT: F 44 LYS cc_start: 0.9039 (mmtp) cc_final: 0.8668 (mmtp) REVERT: G 90 ASP cc_start: 0.8716 (t0) cc_final: 0.8326 (t0) REVERT: K 185 TYR cc_start: 0.8978 (m-80) cc_final: 0.8349 (m-80) outliers start: 16 outliers final: 12 residues processed: 177 average time/residue: 0.0929 time to fit residues: 24.5379 Evaluate side-chains 176 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.067786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044870 restraints weight = 56476.724| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.36 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12650 Z= 0.158 Angle : 0.601 10.697 17928 Z= 0.345 Chirality : 0.044 0.264 2031 Planarity : 0.004 0.039 1592 Dihedral : 29.972 178.156 3313 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.70 % Allowed : 13.21 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.27), residues: 981 helix: 2.30 (0.21), residues: 636 sheet: -0.92 (0.77), residues: 44 loop : -0.48 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.017 0.001 TYR H 41 PHE 0.007 0.001 PHE E 78 TRP 0.006 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (12650) covalent geometry : angle 0.60067 / 0.35 (17928) hydrogen bonds : bond 0.04354 / 2.95 ( 730) hydrogen bonds : angle 3.54512 / 2.54 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9155 (tt0) cc_final: 0.8799 (tt0) REVERT: A 76 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8360 (tp-100) REVERT: B 20 MET cc_start: 0.7890 (tpp) cc_final: 0.7685 (mmm) REVERT: B 44 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8481 (mtpt) REVERT: B 84 MET cc_start: 0.8581 (mmm) cc_final: 0.8198 (tpp) REVERT: C 90 ASP cc_start: 0.8187 (t70) cc_final: 0.7647 (t0) REVERT: C 92 GLU cc_start: 0.8868 (mp0) cc_final: 0.8308 (mp0) REVERT: C 104 GLN cc_start: 0.8267 (mp10) cc_final: 0.7628 (mp10) REVERT: D 51 ASP cc_start: 0.9038 (p0) cc_final: 0.8348 (p0) REVERT: D 62 MET cc_start: 0.9294 (tpp) cc_final: 0.9071 (mmp) REVERT: D 68 ASP cc_start: 0.9239 (t70) cc_final: 0.8908 (t0) REVERT: D 93 GLU cc_start: 0.8937 (mp0) cc_final: 0.8074 (mp0) REVERT: D 123 SER cc_start: 0.8434 (m) cc_final: 0.8021 (p) REVERT: E 50 GLU cc_start: 0.9545 (tt0) cc_final: 0.9308 (tt0) REVERT: E 125 GLN cc_start: 0.9212 (pt0) cc_final: 0.8600 (pm20) REVERT: F 44 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8657 (mmtp) REVERT: G 90 ASP cc_start: 0.8701 (t0) cc_final: 0.8318 (t0) REVERT: H 69 ASP cc_start: 0.9414 (t70) cc_final: 0.9038 (t0) REVERT: K 100 MET cc_start: 0.8514 (mmm) cc_final: 0.8261 (mmm) REVERT: K 185 TYR cc_start: 0.9003 (m-80) cc_final: 0.8381 (m-80) REVERT: K 253 MET cc_start: 0.8026 (mpp) cc_final: 0.7491 (mpp) outliers start: 14 outliers final: 8 residues processed: 181 average time/residue: 0.0997 time to fit residues: 26.3573 Evaluate side-chains 173 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 9.9990 chunk 27 optimal weight: 0.0030 chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.068255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045265 restraints weight = 56642.409| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.38 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12650 Z= 0.141 Angle : 0.593 8.596 17928 Z= 0.341 Chirality : 0.043 0.263 2031 Planarity : 0.004 0.033 1592 Dihedral : 29.910 178.023 3313 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.97 % Allowed : 14.67 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 981 helix: 2.36 (0.20), residues: 634 sheet: -0.87 (0.78), residues: 44 loop : -0.51 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 352 TYR 0.022 0.001 TYR H 41 PHE 0.012 0.001 PHE K 95 TRP 0.007 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (12650) covalent geometry : angle 0.59259 / 0.34 (17928) hydrogen bonds : bond 0.04129 / 2.78 ( 730) hydrogen bonds : angle 3.45810 / 2.47 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.224 Fit side-chains REVERT: A 50 GLU cc_start: 0.9184 (tt0) cc_final: 0.8833 (tt0) REVERT: B 23 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7765 (mmm-85) REVERT: B 44 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8409 (mtpt) REVERT: C 90 ASP cc_start: 0.8217 (t70) cc_final: 0.7579 (t0) REVERT: C 92 GLU cc_start: 0.8779 (mp0) cc_final: 0.8138 (mp0) REVERT: C 104 GLN cc_start: 0.8248 (mp10) cc_final: 0.7613 (mp10) REVERT: D 51 ASP cc_start: 0.9046 (p0) cc_final: 0.8413 (p0) REVERT: D 68 ASP cc_start: 0.9213 (t70) cc_final: 0.8939 (t0) REVERT: D 93 GLU cc_start: 0.8939 (mp0) cc_final: 0.8098 (mp0) REVERT: D 123 SER cc_start: 0.8461 (m) cc_final: 0.8028 (p) REVERT: E 50 GLU cc_start: 0.9543 (tt0) cc_final: 0.9294 (tt0) REVERT: E 77 ASP cc_start: 0.8893 (m-30) cc_final: 0.8666 (m-30) REVERT: E 125 GLN cc_start: 0.9231 (pt0) cc_final: 0.8919 (pt0) REVERT: F 44 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8674 (mmtp) REVERT: G 90 ASP cc_start: 0.8710 (t0) cc_final: 0.8323 (t0) REVERT: H 69 ASP cc_start: 0.9412 (t70) cc_final: 0.9038 (t0) REVERT: K 100 MET cc_start: 0.8626 (mmm) cc_final: 0.8384 (mmm) REVERT: K 185 TYR cc_start: 0.9034 (m-80) cc_final: 0.8410 (m-80) outliers start: 8 outliers final: 8 residues processed: 177 average time/residue: 0.0903 time to fit residues: 23.2149 Evaluate side-chains 179 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.068332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045557 restraints weight = 56274.240| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.34 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12650 Z= 0.141 Angle : 0.597 8.014 17928 Z= 0.340 Chirality : 0.043 0.262 2031 Planarity : 0.004 0.038 1592 Dihedral : 29.848 178.063 3313 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.58 % Allowed : 14.30 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.27), residues: 981 helix: 2.39 (0.20), residues: 635 sheet: -0.82 (0.77), residues: 44 loop : -0.51 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.027 0.001 TYR H 41 PHE 0.007 0.001 PHE A 67 TRP 0.008 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (12650) covalent geometry : angle 0.59694 / 0.34 (17928) hydrogen bonds : bond 0.04066 / 2.74 ( 730) hydrogen bonds : angle 3.41587 / 2.44 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9206 (tt0) cc_final: 0.8832 (tt0) REVERT: A 76 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8386 (tp-100) REVERT: B 23 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7688 (mmm-85) REVERT: B 44 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8340 (mtpt) REVERT: C 29 ARG cc_start: 0.8586 (ttm170) cc_final: 0.8180 (ttm170) REVERT: C 90 ASP cc_start: 0.8194 (t70) cc_final: 0.7490 (t0) REVERT: C 92 GLU cc_start: 0.8797 (mp0) cc_final: 0.8142 (mp0) REVERT: C 104 GLN cc_start: 0.8229 (mp10) cc_final: 0.7586 (mp10) REVERT: D 51 ASP cc_start: 0.9004 (p0) cc_final: 0.8368 (p0) REVERT: D 59 MET cc_start: 0.9482 (tpp) cc_final: 0.9281 (tpt) REVERT: D 68 ASP cc_start: 0.9210 (t70) cc_final: 0.8895 (t0) REVERT: D 93 GLU cc_start: 0.8943 (mp0) cc_final: 0.8085 (mp0) REVERT: D 123 SER cc_start: 0.8453 (m) cc_final: 0.8015 (p) REVERT: E 50 GLU cc_start: 0.9541 (tt0) cc_final: 0.9286 (tt0) REVERT: E 77 ASP cc_start: 0.8908 (m-30) cc_final: 0.8671 (m-30) REVERT: E 125 GLN cc_start: 0.9244 (pt0) cc_final: 0.8686 (pm20) REVERT: F 44 LYS cc_start: 0.9082 (mmtp) cc_final: 0.8677 (mmtp) REVERT: G 90 ASP cc_start: 0.8672 (t0) cc_final: 0.8258 (t0) REVERT: H 69 ASP cc_start: 0.9403 (t70) cc_final: 0.9030 (t0) REVERT: K 100 MET cc_start: 0.8688 (mmm) cc_final: 0.8442 (mmm) REVERT: K 185 TYR cc_start: 0.9034 (m-80) cc_final: 0.8405 (m-80) REVERT: K 241 MET cc_start: 0.8027 (ppp) cc_final: 0.7769 (ppp) REVERT: K 253 MET cc_start: 0.8255 (mpp) cc_final: 0.7759 (mpp) outliers start: 13 outliers final: 12 residues processed: 181 average time/residue: 0.1139 time to fit residues: 29.6021 Evaluate side-chains 181 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.068799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045892 restraints weight = 56174.318| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.37 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12650 Z= 0.134 Angle : 0.592 8.310 17928 Z= 0.338 Chirality : 0.042 0.263 2031 Planarity : 0.004 0.034 1592 Dihedral : 29.768 178.038 3313 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.33 % Allowed : 14.42 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.27), residues: 981 helix: 2.43 (0.20), residues: 634 sheet: -0.74 (0.78), residues: 44 loop : -0.47 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.016 0.001 TYR B 88 PHE 0.009 0.001 PHE D 70 TRP 0.009 0.001 TRP K 218 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (12650) covalent geometry : angle 0.59175 / 0.34 (17928) hydrogen bonds : bond 0.03937 / 2.66 ( 730) hydrogen bonds : angle 3.35352 / 2.40 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9202 (tt0) cc_final: 0.8835 (tt0) REVERT: B 23 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7631 (mmm-85) REVERT: B 84 MET cc_start: 0.8704 (tpp) cc_final: 0.8471 (mmm) REVERT: C 90 ASP cc_start: 0.8211 (t70) cc_final: 0.7474 (t0) REVERT: C 92 GLU cc_start: 0.8799 (mp0) cc_final: 0.8112 (mp0) REVERT: D 51 ASP cc_start: 0.8999 (p0) cc_final: 0.8359 (p0) REVERT: D 59 MET cc_start: 0.9509 (tpp) cc_final: 0.9291 (tpt) REVERT: D 62 MET cc_start: 0.9329 (tpp) cc_final: 0.9100 (mmp) REVERT: D 68 ASP cc_start: 0.9147 (t70) cc_final: 0.8856 (t0) REVERT: D 93 GLU cc_start: 0.8954 (mp0) cc_final: 0.8088 (mp0) REVERT: D 123 SER cc_start: 0.8581 (m) cc_final: 0.8112 (p) REVERT: E 50 GLU cc_start: 0.9545 (tt0) cc_final: 0.9288 (tt0) REVERT: E 77 ASP cc_start: 0.8865 (m-30) cc_final: 0.8620 (m-30) REVERT: E 125 GLN cc_start: 0.9243 (pt0) cc_final: 0.8951 (pt0) REVERT: F 44 LYS cc_start: 0.9000 (mmtp) cc_final: 0.8506 (mmtp) REVERT: G 90 ASP cc_start: 0.8647 (t0) cc_final: 0.8223 (t0) REVERT: H 69 ASP cc_start: 0.9406 (t70) cc_final: 0.9030 (t0) REVERT: H 110 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8727 (m90) REVERT: K 100 MET cc_start: 0.8746 (mmm) cc_final: 0.8515 (mmm) REVERT: K 185 TYR cc_start: 0.9032 (m-80) cc_final: 0.8405 (m-80) REVERT: K 241 MET cc_start: 0.7966 (ppp) cc_final: 0.7724 (ppp) outliers start: 11 outliers final: 9 residues processed: 180 average time/residue: 0.1071 time to fit residues: 28.3632 Evaluate side-chains 185 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.068665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.045743 restraints weight = 56077.600| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.38 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12650 Z= 0.140 Angle : 0.587 8.710 17928 Z= 0.335 Chirality : 0.042 0.262 2031 Planarity : 0.004 0.041 1592 Dihedral : 29.745 178.158 3313 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.33 % Allowed : 15.15 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.27), residues: 981 helix: 2.44 (0.20), residues: 634 sheet: -0.69 (0.79), residues: 44 loop : -0.48 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 99 TYR 0.024 0.001 TYR D 83 PHE 0.007 0.001 PHE A 67 TRP 0.010 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (12650) covalent geometry : angle 0.58714 / 0.34 (17928) hydrogen bonds : bond 0.03944 / 2.65 ( 730) hydrogen bonds : angle 3.33460 / 2.39 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9218 (tt0) cc_final: 0.8829 (tt0) REVERT: A 76 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8400 (tp-100) REVERT: B 44 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8432 (mtpt) REVERT: B 84 MET cc_start: 0.8514 (tpp) cc_final: 0.7474 (mmm) REVERT: C 29 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8171 (ttm170) REVERT: C 90 ASP cc_start: 0.8239 (t70) cc_final: 0.7507 (t0) REVERT: C 92 GLU cc_start: 0.8816 (mp0) cc_final: 0.8149 (mp0) REVERT: D 51 ASP cc_start: 0.9007 (p0) cc_final: 0.8360 (p0) REVERT: D 59 MET cc_start: 0.9512 (tpp) cc_final: 0.9299 (tpt) REVERT: D 62 MET cc_start: 0.9285 (tpp) cc_final: 0.9071 (mmp) REVERT: D 68 ASP cc_start: 0.9174 (t70) cc_final: 0.8858 (t0) REVERT: D 93 GLU cc_start: 0.8949 (mp0) cc_final: 0.8085 (mp0) REVERT: D 123 SER cc_start: 0.8585 (m) cc_final: 0.8119 (p) REVERT: E 50 GLU cc_start: 0.9542 (tt0) cc_final: 0.9283 (tt0) REVERT: E 125 GLN cc_start: 0.9252 (pt0) cc_final: 0.8970 (pt0) REVERT: F 44 LYS cc_start: 0.9000 (mmtp) cc_final: 0.8565 (mmtp) REVERT: G 90 ASP cc_start: 0.8643 (t0) cc_final: 0.8214 (t0) REVERT: H 69 ASP cc_start: 0.9400 (t70) cc_final: 0.9022 (t0) REVERT: K 100 MET cc_start: 0.8768 (mmm) cc_final: 0.8533 (mmm) REVERT: K 185 TYR cc_start: 0.9015 (m-80) cc_final: 0.8391 (m-80) REVERT: K 241 MET cc_start: 0.7975 (ppp) cc_final: 0.7753 (ppp) REVERT: K 253 MET cc_start: 0.8225 (mpp) cc_final: 0.7731 (mpp) outliers start: 11 outliers final: 11 residues processed: 181 average time/residue: 0.1118 time to fit residues: 29.1982 Evaluate side-chains 185 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045182 restraints weight = 56666.480| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.37 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12650 Z= 0.170 Angle : 0.607 8.283 17928 Z= 0.344 Chirality : 0.043 0.263 2031 Planarity : 0.004 0.038 1592 Dihedral : 29.777 178.457 3313 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.33 % Allowed : 15.15 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.27), residues: 981 helix: 2.45 (0.21), residues: 636 sheet: -0.72 (0.78), residues: 44 loop : -0.46 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.023 0.001 TYR B 88 PHE 0.010 0.001 PHE E 78 TRP 0.010 0.001 TRP K 218 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (12650) covalent geometry : angle 0.60662 / 0.34 (17928) hydrogen bonds : bond 0.04161 / 2.80 ( 730) hydrogen bonds : angle 3.39875 / 2.44 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9223 (tt0) cc_final: 0.8814 (tt0) REVERT: A 76 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8339 (tp-100) REVERT: B 44 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8429 (mtpt) REVERT: C 29 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8358 (ttm170) REVERT: C 90 ASP cc_start: 0.8249 (t70) cc_final: 0.7493 (t0) REVERT: C 92 GLU cc_start: 0.8798 (mp0) cc_final: 0.8112 (mp0) REVERT: C 104 GLN cc_start: 0.8237 (mp10) cc_final: 0.7666 (mp10) REVERT: D 35 GLU cc_start: 0.7226 (tm-30) cc_final: 0.7007 (tm-30) REVERT: D 51 ASP cc_start: 0.8983 (p0) cc_final: 0.8307 (p0) REVERT: D 59 MET cc_start: 0.9513 (tpp) cc_final: 0.9272 (tpp) REVERT: D 62 MET cc_start: 0.9262 (tpp) cc_final: 0.9062 (mmp) REVERT: D 68 ASP cc_start: 0.9224 (t70) cc_final: 0.8956 (t0) REVERT: D 123 SER cc_start: 0.8623 (m) cc_final: 0.8161 (p) REVERT: E 50 GLU cc_start: 0.9545 (tt0) cc_final: 0.9006 (tt0) REVERT: E 125 GLN cc_start: 0.9271 (pt0) cc_final: 0.9009 (pt0) REVERT: F 44 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8608 (mmtp) REVERT: G 90 ASP cc_start: 0.8667 (t0) cc_final: 0.8239 (t0) REVERT: H 69 ASP cc_start: 0.9414 (t70) cc_final: 0.9032 (t0) REVERT: H 110 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8659 (m90) REVERT: K 100 MET cc_start: 0.8789 (mmm) cc_final: 0.8553 (mmm) REVERT: K 241 MET cc_start: 0.7987 (ppp) cc_final: 0.7769 (ppp) REVERT: K 253 MET cc_start: 0.8181 (mpp) cc_final: 0.7723 (mpp) outliers start: 11 outliers final: 10 residues processed: 178 average time/residue: 0.1117 time to fit residues: 28.7729 Evaluate side-chains 183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045694 restraints weight = 56388.241| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.38 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12650 Z= 0.139 Angle : 0.585 8.101 17928 Z= 0.335 Chirality : 0.042 0.264 2031 Planarity : 0.004 0.034 1592 Dihedral : 29.763 178.459 3313 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.33 % Allowed : 15.64 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.27), residues: 981 helix: 2.45 (0.20), residues: 635 sheet: -0.74 (0.77), residues: 44 loop : -0.47 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.038 0.001 TYR B 88 PHE 0.008 0.001 PHE E 78 TRP 0.011 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (12650) covalent geometry : angle 0.58495 / 0.33 (17928) hydrogen bonds : bond 0.03924 / 2.65 ( 730) hydrogen bonds : angle 3.32931 / 2.38 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.18 seconds wall clock time: 37 minutes 4.94 seconds (2224.94 seconds total)