Starting phenix.real_space_refine on Sun Aug 24 03:34:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o61_70156/08_2025/9o61_70156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o61_70156/08_2025/9o61_70156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o61_70156/08_2025/9o61_70156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o61_70156/08_2025/9o61_70156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o61_70156/08_2025/9o61_70156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o61_70156/08_2025/9o61_70156.map" } resolution = 1.68 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= 0.038 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 10338 2.51 5 N 2754 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16392 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "B" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "C" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "D" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "E" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "F" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "G" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "H" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "I" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "J" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "K" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "L" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'PEB': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 1, 'PUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 1, 'PUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.13, per 1000 atoms: 0.25 Number of scatterers: 16392 At special positions: 0 Unit cell: (132.02, 119.72, 72.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3186 8.00 N 2754 7.00 C 10338 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 634.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 20 through 47 removed outlier: 4.279A pdb=" N ALA A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 75 through 100 Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.855A pdb=" N TYR A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.796A pdb=" N LYS B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.530A pdb=" N ASN B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 20 through 63 removed outlier: 4.310A pdb=" N ALA C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.854A pdb=" N TYR C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 164 Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 33 through 47 removed outlier: 3.549A pdb=" N ASN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 109 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 20 through 47 removed outlier: 4.314A pdb=" N ALA E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 75 through 100 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 123 through 138 removed outlier: 3.899A pdb=" N TYR E 127 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 164 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.977A pdb=" N LYS F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 33 through 46 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 64 through 67 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 123 through 143 Processing helix chain 'F' and resid 158 through 176 Processing helix chain 'G' and resid 3 through 16 Processing helix chain 'G' and resid 20 through 47 removed outlier: 4.312A pdb=" N ALA G 35 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 75 through 100 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 112 through 120 Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.981A pdb=" N TYR G 127 " --> pdb=" O PRO G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 164 Processing helix chain 'H' and resid 3 through 14 Processing helix chain 'H' and resid 20 through 33 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.588A pdb=" N ILE H 67 " --> pdb=" O PRO H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 75 through 100 Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 123 through 143 Processing helix chain 'H' and resid 158 through 176 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 20 through 63 removed outlier: 4.325A pdb=" N ALA I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA I 50 " --> pdb=" O GLY I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 75 through 100 Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'I' and resid 123 through 138 removed outlier: 3.942A pdb=" N TYR I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.957A pdb=" N LYS J 15 " --> pdb=" O ASN J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 33 through 47 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 143 Processing helix chain 'J' and resid 158 through 176 Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 20 through 47 removed outlier: 4.365A pdb=" N ALA K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 75 through 100 Processing helix chain 'K' and resid 102 through 109 Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 123 through 138 removed outlier: 3.925A pdb=" N TYR K 127 " --> pdb=" O PRO K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 164 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.947A pdb=" N LYS L 15 " --> pdb=" O ASN L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 33 Processing helix chain 'L' and resid 33 through 46 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 64 through 67 Processing helix chain 'L' and resid 75 through 100 Processing helix chain 'L' and resid 102 through 109 Processing helix chain 'L' and resid 112 through 121 Processing helix chain 'L' and resid 123 through 143 Processing helix chain 'L' and resid 158 through 176 1266 hydrogen bonds defined for protein. 3747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 2.20 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: 3414 1.33 - 1.45: 3851 1.45 - 1.57: 9259 1.57 - 1.69: 0 1.69 - 1.82: 162 Bond restraints: 16686 Sorted by residual: bond pdb=" C3C PUB B 201 " pdb=" C4C PUB B 201 " ideal model delta sigma weight residual 1.450 1.380 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C PUB H 201 " pdb=" C4C PUB H 201 " ideal model delta sigma weight residual 1.450 1.381 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C3C PUB D 201 " pdb=" C4C PUB D 201 " ideal model delta sigma weight residual 1.450 1.381 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C3C PUB F 201 " pdb=" C4C PUB F 201 " ideal model delta sigma weight residual 1.450 1.381 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C3C PUB J 201 " pdb=" C4C PUB J 201 " ideal model delta sigma weight residual 1.450 1.382 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 21875 1.61 - 3.22: 677 3.22 - 4.82: 129 4.82 - 6.43: 44 6.43 - 8.04: 9 Bond angle restraints: 22734 Sorted by residual: angle pdb=" N THR B 145 " pdb=" CA THR B 145 " pdb=" C THR B 145 " ideal model delta sigma weight residual 113.72 107.59 6.13 1.30e+00 5.92e-01 2.22e+01 angle pdb=" CA ARG G 33 " pdb=" C ARG G 33 " pdb=" O ARG G 33 " ideal model delta sigma weight residual 121.00 117.26 3.74 1.05e+00 9.07e-01 1.27e+01 angle pdb=" N ASN D 35 " pdb=" CA ASN D 35 " pdb=" C ASN D 35 " ideal model delta sigma weight residual 111.71 115.59 -3.88 1.15e+00 7.56e-01 1.14e+01 angle pdb=" C ASN D 35 " pdb=" N LYS D 36 " pdb=" CA LYS D 36 " ideal model delta sigma weight residual 120.44 116.09 4.35 1.30e+00 5.92e-01 1.12e+01 angle pdb=" CA MET C 144 " pdb=" C MET C 144 " pdb=" O MET C 144 " ideal model delta sigma weight residual 121.45 118.14 3.31 1.07e+00 8.73e-01 9.58e+00 ... (remaining 22729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9803 17.66 - 35.32: 942 35.32 - 52.98: 200 52.98 - 70.65: 60 70.65 - 88.31: 23 Dihedral angle restraints: 11028 sinusoidal: 5124 harmonic: 5904 Sorted by residual: dihedral pdb=" CD ARG E 142 " pdb=" NE ARG E 142 " pdb=" CZ ARG E 142 " pdb=" NH1 ARG E 142 " ideal model delta sinusoidal sigma weight residual 0.00 -39.93 39.93 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA VAL E 140 " pdb=" C VAL E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual 0.00 -21.81 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL C 140 " pdb=" C VAL C 140 " pdb=" N PRO C 141 " pdb=" CA PRO C 141 " ideal model delta harmonic sigma weight residual 0.00 -18.18 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 11025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2089 0.054 - 0.107: 357 0.107 - 0.161: 25 0.161 - 0.214: 11 0.214 - 0.268: 2 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C1D PEB D 203 " pdb=" ND PEB D 203 " pdb=" C2D PEB D 203 " pdb=" CHC PEB D 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.83 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ASN D 35 " pdb=" N ASN D 35 " pdb=" C ASN D 35 " pdb=" CB ASN D 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C4A PUB L 201 " pdb=" C3A PUB L 201 " pdb=" CHA PUB L 201 " pdb=" NA PUB L 201 " both_signs ideal model delta sigma weight residual False 2.57 2.78 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2481 not shown) Planarity restraints: 2898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PEB D 203 " -0.314 2.00e-02 2.50e+03 3.81e-01 3.27e+03 pdb=" C1B PEB D 203 " 0.043 2.00e-02 2.50e+03 pdb=" C2B PEB D 203 " -0.151 2.00e-02 2.50e+03 pdb=" C3B PEB D 203 " 0.124 2.00e-02 2.50e+03 pdb=" C4B PEB D 203 " -0.128 2.00e-02 2.50e+03 pdb=" CAB PEB D 203 " 0.607 2.00e-02 2.50e+03 pdb=" CHA PEB D 203 " 0.618 2.00e-02 2.50e+03 pdb=" CHB PEB D 203 " -0.193 2.00e-02 2.50e+03 pdb=" CMB PEB D 203 " -0.606 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A PEB D 203 " 0.041 2.00e-02 2.50e+03 1.76e-01 3.86e+02 pdb=" C2A PEB D 203 " 0.079 2.00e-02 2.50e+03 pdb=" C4A PEB D 203 " -0.227 2.00e-02 2.50e+03 pdb=" NA PEB D 203 " 0.265 2.00e-02 2.50e+03 pdb=" OA PEB D 203 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A PUB B 201 " -0.037 2.00e-02 2.50e+03 1.22e-01 1.86e+02 pdb=" C2A PUB B 201 " -0.054 2.00e-02 2.50e+03 pdb=" C4A PUB B 201 " 0.154 2.00e-02 2.50e+03 pdb=" NA PUB B 201 " -0.181 2.00e-02 2.50e+03 pdb=" OA PUB B 201 " 0.118 2.00e-02 2.50e+03 ... (remaining 2895 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 78 2.40 - 3.02: 10143 3.02 - 3.65: 29904 3.65 - 4.27: 43180 4.27 - 4.90: 70300 Nonbonded interactions: 153605 Sorted by model distance: nonbonded pdb=" NH2 ARG C 142 " pdb=" OD1 ASP C 143 " model vdw 1.774 3.120 nonbonded pdb=" NZ LYS C 43 " pdb=" C4D PEB C 202 " model vdw 2.113 2.672 nonbonded pdb=" OD1 ASP H 13 " pdb=" OH TYR L 74 " model vdw 2.183 3.040 nonbonded pdb=" O TYR H 74 " pdb=" OG1 THR H 75 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP E 57 " pdb=" OH TYR E 83 " model vdw 2.214 3.040 ... (remaining 153600 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 1 through 202) selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 202) selection = (chain 'F' and resid 1 through 202) selection = (chain 'H' and resid 1 through 202) selection = chain 'J' selection = (chain 'L' and resid 1 through 202) } 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: 2.980 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.610 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 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 : 0.004 0.070 16719 Z= 0.238 Angle : 0.697 8.040 22734 Z= 0.356 Chirality : 0.040 0.268 2484 Planarity : 0.012 0.381 2898 Dihedral : 14.951 88.306 7236 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.29 % Favored : 98.36 % Rotamer: Outliers : 0.94 % Allowed : 9.55 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.20 (0.18), residues: 2016 helix: 1.84 (0.12), residues: 1626 sheet: None (None), residues: 0 loop : -0.07 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 33 TYR 0.025 0.001 TYR L 74 PHE 0.013 0.002 PHE I 152 TRP 0.005 0.001 TRP C 108 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00424 (16686) covalent geometry : angle 0.69677 (22734) hydrogen bonds : bond 0.09343 ( 1266) hydrogen bonds : angle 4.64466 ( 3747) Misc. bond : bond 0.01219 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 407 time to evaluate : 0.640 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: A 37 ARG cc_start: 0.8791 (ptt90) cc_final: 0.8531 (ptt90) REVERT: A 49 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8091 (mp0) REVERT: A 53 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8632 (tttm) REVERT: A 71 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 84 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8252 (ttp80) REVERT: G 53 LYS cc_start: 0.7914 (tttt) cc_final: 0.7508 (tttm) REVERT: G 57 ASP cc_start: 0.8278 (m-30) cc_final: 0.8052 (m-30) REVERT: G 71 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8252 (mm-30) REVERT: G 77 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7181 (tm-30) REVERT: H 84 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8295 (ttm110) outliers start: 15 outliers final: 3 residues processed: 415 average time/residue: 0.8036 time to fit residues: 361.4872 Evaluate side-chains 343 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 162 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN G 48 HIS G 76 GLN H 72 ASN H 125 ASN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086171 restraints weight = 19052.921| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 0.93 r_work: 0.3027 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16719 Z= 0.182 Angle : 0.635 8.014 22734 Z= 0.311 Chirality : 0.038 0.185 2484 Planarity : 0.004 0.048 2898 Dihedral : 10.515 84.132 3921 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.60 % Allowed : 1.14 % Favored : 98.26 % Rotamer: Outliers : 1.19 % Allowed : 10.05 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.14 (0.18), residues: 2016 helix: 1.70 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : 0.26 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 142 TYR 0.020 0.002 TYR L 74 PHE 0.010 0.002 PHE G 152 TRP 0.005 0.001 TRP C 108 HIS 0.005 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00377 (16686) covalent geometry : angle 0.63475 (22734) hydrogen bonds : bond 0.04811 ( 1266) hydrogen bonds : angle 4.50230 ( 3747) Misc. bond : bond 0.00429 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 367 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8436 (mp0) REVERT: A 71 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 84 ARG cc_start: 0.8710 (ttp-110) cc_final: 0.8280 (ttm110) REVERT: E 53 LYS cc_start: 0.8979 (tttm) cc_final: 0.8753 (tmtm) REVERT: G 71 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8634 (mm-30) REVERT: H 25 GLN cc_start: 0.8334 (tp40) cc_final: 0.8116 (tp-100) REVERT: H 84 ARG cc_start: 0.8963 (ttp-110) cc_final: 0.8470 (ttm110) outliers start: 19 outliers final: 7 residues processed: 379 average time/residue: 0.8492 time to fit residues: 348.1289 Evaluate side-chains 341 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 334 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 174 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 127 optimal weight: 0.0270 chunk 189 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN G 32 GLN H 72 ASN H 125 ASN I 32 GLN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087863 restraints weight = 20504.191| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.94 r_work: 0.3116 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16719 Z= 0.163 Angle : 0.605 7.969 22734 Z= 0.297 Chirality : 0.038 0.189 2484 Planarity : 0.005 0.147 2898 Dihedral : 10.359 85.263 3920 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.89 % Favored : 98.51 % Rotamer: Outliers : 0.94 % Allowed : 10.17 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.24 (0.18), residues: 2016 helix: 1.76 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : 0.31 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 142 TYR 0.020 0.001 TYR L 74 PHE 0.009 0.002 PHE G 152 TRP 0.003 0.001 TRP K 108 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00336 (16686) covalent geometry : angle 0.60511 (22734) hydrogen bonds : bond 0.04587 ( 1266) hydrogen bonds : angle 4.43856 ( 3747) Misc. bond : bond 0.00419 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 347 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8340 (mm-30) REVERT: B 25 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8174 (tp40) REVERT: B 84 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8310 (ttp-110) REVERT: C 118 ARG cc_start: 0.8448 (ptp-170) cc_final: 0.8220 (mtp85) REVERT: E 32 GLN cc_start: 0.8590 (tp40) cc_final: 0.8313 (mm110) REVERT: H 84 ARG cc_start: 0.8912 (ttp-110) cc_final: 0.8514 (ttm110) outliers start: 15 outliers final: 8 residues processed: 355 average time/residue: 0.7154 time to fit residues: 275.3110 Evaluate side-chains 331 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 126 optimal weight: 0.0070 chunk 179 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 30 ASN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN H 72 ASN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.082225 restraints weight = 19065.045| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 0.93 r_work: 0.2970 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16719 Z= 0.246 Angle : 0.688 8.633 22734 Z= 0.333 Chirality : 0.041 0.204 2484 Planarity : 0.004 0.094 2898 Dihedral : 10.636 79.051 3920 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.84 % Favored : 98.56 % Rotamer: Outliers : 1.31 % Allowed : 9.43 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.06 (0.18), residues: 2016 helix: 1.62 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : 0.36 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 142 TYR 0.021 0.002 TYR J 74 PHE 0.011 0.003 PHE C 131 TRP 0.005 0.002 TRP K 108 HIS 0.005 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00520 (16686) covalent geometry : angle 0.68771 (22734) hydrogen bonds : bond 0.05268 ( 1266) hydrogen bonds : angle 4.65380 ( 3747) Misc. bond : bond 0.00599 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 351 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8462 (mm-30) REVERT: B 25 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8086 (tp40) REVERT: B 84 ARG cc_start: 0.8749 (ttp-110) cc_final: 0.8387 (ttm110) REVERT: C 118 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.8371 (mtp85) REVERT: H 25 GLN cc_start: 0.8327 (tp-100) cc_final: 0.8119 (tp40) REVERT: H 84 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8481 (ttm110) outliers start: 21 outliers final: 9 residues processed: 364 average time/residue: 0.7200 time to fit residues: 284.2231 Evaluate side-chains 338 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 329 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 chunk 75 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN G 76 GLN H 72 ASN I 32 GLN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.087181 restraints weight = 19209.829| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 0.93 r_work: 0.3066 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16719 Z= 0.156 Angle : 0.605 8.198 22734 Z= 0.297 Chirality : 0.038 0.192 2484 Planarity : 0.004 0.052 2898 Dihedral : 10.499 77.348 3920 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.84 % Favored : 98.56 % Rotamer: Outliers : 1.06 % Allowed : 9.61 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.27 (0.18), residues: 2016 helix: 1.78 (0.12), residues: 1668 sheet: None (None), residues: 0 loop : 0.34 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 142 TYR 0.021 0.001 TYR F 74 PHE 0.009 0.002 PHE G 152 TRP 0.003 0.001 TRP A 108 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00326 (16686) covalent geometry : angle 0.60542 (22734) hydrogen bonds : bond 0.04484 ( 1266) hydrogen bonds : angle 4.44395 ( 3747) Misc. bond : bond 0.00418 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 351 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8944 (ptt90) cc_final: 0.8736 (ptt90) REVERT: A 71 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8444 (mm-30) REVERT: B 25 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8076 (tp40) REVERT: B 84 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8304 (ttp-110) REVERT: C 118 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8224 (mtp85) REVERT: H 25 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8007 (tp-100) REVERT: H 84 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8500 (ttm110) outliers start: 17 outliers final: 12 residues processed: 362 average time/residue: 0.8204 time to fit residues: 320.6739 Evaluate side-chains 348 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 335 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain K residue 59 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 171 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 195 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085548 restraints weight = 19176.472| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.93 r_work: 0.3038 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16719 Z= 0.176 Angle : 0.623 9.349 22734 Z= 0.304 Chirality : 0.039 0.195 2484 Planarity : 0.004 0.038 2898 Dihedral : 10.428 76.106 3920 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.94 % Favored : 98.46 % Rotamer: Outliers : 1.19 % Allowed : 10.74 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.30 (0.18), residues: 2016 helix: 1.80 (0.12), residues: 1668 sheet: None (None), residues: 0 loop : 0.39 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 142 TYR 0.024 0.001 TYR J 74 PHE 0.008 0.002 PHE G 152 TRP 0.003 0.001 TRP C 108 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00369 (16686) covalent geometry : angle 0.62278 (22734) hydrogen bonds : bond 0.04655 ( 1266) hydrogen bonds : angle 4.47394 ( 3747) Misc. bond : bond 0.00450 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 25 GLN cc_start: 0.8306 (tp-100) cc_final: 0.8060 (tp40) REVERT: B 84 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8327 (ttp-110) REVERT: H 25 GLN cc_start: 0.8320 (tp-100) cc_final: 0.8057 (tp40) REVERT: H 84 ARG cc_start: 0.8966 (ttp-110) cc_final: 0.8498 (ttm110) outliers start: 19 outliers final: 13 residues processed: 357 average time/residue: 0.8417 time to fit residues: 325.3176 Evaluate side-chains 337 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 324 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 59 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 151 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN I 32 GLN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085267 restraints weight = 19132.394| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 0.93 r_work: 0.3032 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16719 Z= 0.182 Angle : 0.629 7.943 22734 Z= 0.308 Chirality : 0.039 0.198 2484 Planarity : 0.004 0.038 2898 Dihedral : 10.430 75.575 3920 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.79 % Favored : 98.61 % Rotamer: Outliers : 1.06 % Allowed : 11.11 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.25 (0.18), residues: 2016 helix: 1.76 (0.12), residues: 1668 sheet: None (None), residues: 0 loop : 0.41 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 78 TYR 0.024 0.002 TYR F 74 PHE 0.008 0.002 PHE L 30 TRP 0.004 0.001 TRP C 108 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00382 (16686) covalent geometry : angle 0.62938 (22734) hydrogen bonds : bond 0.04709 ( 1266) hydrogen bonds : angle 4.49660 ( 3747) Misc. bond : bond 0.00465 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 340 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8452 (mm-30) REVERT: B 25 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8034 (tp-100) REVERT: B 84 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: H 25 GLN cc_start: 0.8310 (tp-100) cc_final: 0.8046 (tp40) REVERT: H 84 ARG cc_start: 0.8962 (ttp-110) cc_final: 0.8496 (ttm110) REVERT: K 53 LYS cc_start: 0.8593 (tttm) cc_final: 0.8363 (tttm) outliers start: 17 outliers final: 13 residues processed: 353 average time/residue: 0.8309 time to fit residues: 317.2549 Evaluate side-chains 341 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 328 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 59 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 127 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN H 72 ASN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085788 restraints weight = 19213.452| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 0.94 r_work: 0.3041 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16719 Z= 0.174 Angle : 0.630 8.215 22734 Z= 0.309 Chirality : 0.039 0.200 2484 Planarity : 0.004 0.040 2898 Dihedral : 10.435 79.546 3920 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.79 % Favored : 98.61 % Rotamer: Outliers : 1.06 % Allowed : 11.24 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.28 (0.18), residues: 2016 helix: 1.77 (0.12), residues: 1668 sheet: None (None), residues: 0 loop : 0.44 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.026 0.001 TYR F 74 PHE 0.008 0.002 PHE L 30 TRP 0.003 0.001 TRP C 108 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00364 (16686) covalent geometry : angle 0.62987 (22734) hydrogen bonds : bond 0.04632 ( 1266) hydrogen bonds : angle 4.48194 ( 3747) Misc. bond : bond 0.00456 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 342 time to evaluate : 0.719 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: A 71 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8430 (mm-30) REVERT: B 25 GLN cc_start: 0.8286 (tp-100) cc_final: 0.8022 (tp-100) REVERT: B 84 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8316 (ttp-110) REVERT: H 25 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8044 (tp40) REVERT: H 84 ARG cc_start: 0.8958 (ttp-110) cc_final: 0.8498 (ttm110) REVERT: K 53 LYS cc_start: 0.8621 (tttm) cc_final: 0.8413 (tttm) REVERT: K 54 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8046 (tt0) outliers start: 17 outliers final: 14 residues processed: 354 average time/residue: 0.8791 time to fit residues: 336.5892 Evaluate side-chains 343 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 329 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 59 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 170 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN I 32 GLN I 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085702 restraints weight = 19079.978| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 0.93 r_work: 0.3040 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16719 Z= 0.177 Angle : 0.641 8.777 22734 Z= 0.314 Chirality : 0.039 0.211 2484 Planarity : 0.004 0.042 2898 Dihedral : 10.416 77.806 3920 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.84 % Favored : 98.56 % Rotamer: Outliers : 0.94 % Allowed : 11.67 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.27 (0.18), residues: 2016 helix: 1.77 (0.12), residues: 1668 sheet: None (None), residues: 0 loop : 0.46 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 118 TYR 0.027 0.002 TYR F 74 PHE 0.008 0.002 PHE L 30 TRP 0.004 0.001 TRP C 108 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00374 (16686) covalent geometry : angle 0.64089 (22734) hydrogen bonds : bond 0.04654 ( 1266) hydrogen bonds : angle 4.49031 ( 3747) Misc. bond : bond 0.00465 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8450 (mm-30) REVERT: B 25 GLN cc_start: 0.8286 (tp-100) cc_final: 0.8021 (tp-100) REVERT: B 84 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8316 (ttp-110) REVERT: H 25 GLN cc_start: 0.8304 (tp-100) cc_final: 0.8042 (tp40) REVERT: H 84 ARG cc_start: 0.8966 (ttp-110) cc_final: 0.8499 (ttm110) outliers start: 15 outliers final: 14 residues processed: 343 average time/residue: 0.8546 time to fit residues: 317.0653 Evaluate side-chains 337 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 323 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 59 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 129 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 159 optimal weight: 0.1980 chunk 109 optimal weight: 0.0270 chunk 168 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN I 32 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** 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 = 0.3325 r_free = 0.3325 target = 0.096075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088462 restraints weight = 19207.597| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 0.93 r_work: 0.3094 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16719 Z= 0.150 Angle : 0.617 7.918 22734 Z= 0.304 Chirality : 0.038 0.205 2484 Planarity : 0.004 0.044 2898 Dihedral : 10.400 84.004 3920 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.14 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 12.11 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.38 (0.18), residues: 2016 helix: 1.82 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : 0.56 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 78 TYR 0.028 0.001 TYR L 74 PHE 0.009 0.002 PHE G 152 TRP 0.003 0.001 TRP I 108 HIS 0.005 0.002 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00314 (16686) covalent geometry : angle 0.61743 (22734) hydrogen bonds : bond 0.04330 ( 1266) hydrogen bonds : angle 4.40046 ( 3747) Misc. bond : bond 0.00409 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 339 time to evaluate : 0.589 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: A 37 ARG cc_start: 0.8851 (ptt90) cc_final: 0.8599 (ptt90) REVERT: A 71 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 25 GLN cc_start: 0.8282 (tp-100) cc_final: 0.8021 (tp-100) REVERT: B 84 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8304 (ttp-110) REVERT: G 151 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8631 (mm-30) REVERT: H 25 GLN cc_start: 0.8302 (tp-100) cc_final: 0.8045 (tp40) REVERT: H 84 ARG cc_start: 0.8920 (ttp-110) cc_final: 0.8485 (ttm110) outliers start: 14 outliers final: 13 residues processed: 349 average time/residue: 0.7820 time to fit residues: 294.5268 Evaluate side-chains 337 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 324 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 59 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 50 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN H 72 ASN I 32 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083688 restraints weight = 18962.239| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 0.93 r_work: 0.2997 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16719 Z= 0.223 Angle : 0.698 9.257 22734 Z= 0.341 Chirality : 0.041 0.214 2484 Planarity : 0.004 0.047 2898 Dihedral : 10.498 79.590 3920 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.60 % Allowed : 0.74 % Favored : 98.66 % Rotamer: Outliers : 1.00 % Allowed : 12.61 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.15 (0.18), residues: 2016 helix: 1.66 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : 0.55 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 78 TYR 0.025 0.002 TYR F 74 PHE 0.011 0.002 PHE C 131 TRP 0.005 0.002 TRP K 108 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00472 (16686) covalent geometry : angle 0.69791 (22734) hydrogen bonds : bond 0.05021 ( 1266) hydrogen bonds : angle 4.60846 ( 3747) Misc. bond : bond 0.00576 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8596.30 seconds wall clock time: 146 minutes 58.71 seconds (8818.71 seconds total)