Starting phenix.real_space_refine on Thu Aug 6 12:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2p_53536/08_2026/9r2p_53536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2p_53536/08_2026/9r2p_53536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2p_53536/08_2026/9r2p_53536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2p_53536/08_2026/9r2p_53536.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2p_53536/08_2026/9r2p_53536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2p_53536/08_2026/9r2p_53536.cif" } resolution = 4.18 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= -0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 262 5.49 5 S 14 5.16 5 C 8803 2.51 5 N 2948 2.21 5 O 3433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15460 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2667 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2704 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "L" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "M" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "N" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Time building chain proxies: 3.38, per 1000 atoms: 0.22 Number of scatterers: 15460 At special positions: 0 Unit cell: (128.037, 195.975, 128.908, 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 14 16.00 P 262 15.00 O 3433 8.00 N 2948 7.00 C 8803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 598.7 milliseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 18 sheets defined 41.6% alpha, 15.3% beta 131 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.612A pdb=" N ARG A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.380A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.542A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.515A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 46 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.657A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.543A pdb=" N ARG F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 78 removed outlier: 3.649A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.952A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 36 removed outlier: 3.624A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.563A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 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 125 removed outlier: 3.524A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.975A pdb=" N TYR K 107 " --> pdb=" O GLN K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 289 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 289 Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 289 removed outlier: 3.572A pdb=" N LEU M 289 " --> pdb=" O GLU M 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 289 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.085A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.225A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.941A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.010A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 113 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.213A pdb=" N MET K 133 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N CYS K 275 " --> pdb=" O MET K 133 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS K 135 " --> pdb=" O CYS K 275 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 6.238A pdb=" N LEU L 257 " --> pdb=" O LEU L 265 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG L 267 " --> pdb=" O ILE L 255 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE L 255 " --> pdb=" O ARG L 267 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER L 269 " --> pdb=" O THR L 253 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR L 253 " --> pdb=" O SER L 269 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU L 271 " --> pdb=" O ILE L 251 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE L 251 " --> pdb=" O GLU L 271 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.772A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 113 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 6.403A pdb=" N LEU N 257 " --> pdb=" O LEU N 265 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG N 267 " --> pdb=" O ILE N 255 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE N 255 " --> pdb=" O ARG N 267 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER N 269 " --> pdb=" O THR N 253 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR N 253 " --> pdb=" O SER N 269 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU N 271 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE N 251 " --> pdb=" O GLU N 271 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 1.62 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: 3082 1.33 - 1.45: 4633 1.45 - 1.57: 7997 1.57 - 1.69: 513 1.69 - 1.81: 24 Bond restraints: 16249 Sorted by residual: bond pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.72e+01 bond pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " ideal model delta sigma weight residual 1.435 1.368 0.067 1.30e-02 5.92e+03 2.63e+01 bond pdb=" C3' DG J 79 " pdb=" O3' DG J 79 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" C3' DC J 99 " pdb=" O3' DC J 99 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" C3' DA I 68 " pdb=" C2' DA I 68 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.90e+01 ... (remaining 16244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20915 1.61 - 3.22: 1873 3.22 - 4.84: 412 4.84 - 6.45: 60 6.45 - 8.06: 11 Bond angle restraints: 23271 Sorted by residual: angle pdb=" O5' DG J 22 " pdb=" C5' DG J 22 " pdb=" C4' DG J 22 " ideal model delta sigma weight residual 109.40 113.86 -4.46 8.00e-01 1.56e+00 3.11e+01 angle pdb=" C3' DC J 78 " pdb=" O3' DC J 78 " pdb=" P DG J 79 " ideal model delta sigma weight residual 119.70 126.08 -6.38 1.20e+00 6.94e-01 2.82e+01 angle pdb=" C3' DG I 99 " pdb=" O3' DG I 99 " pdb=" P DG I 100 " ideal model delta sigma weight residual 119.70 125.79 -6.09 1.20e+00 6.94e-01 2.57e+01 angle pdb=" O5' DG J 12 " pdb=" C5' DG J 12 " pdb=" C4' DG J 12 " ideal model delta sigma weight residual 109.40 113.21 -3.81 8.00e-01 1.56e+00 2.27e+01 angle pdb=" O5' DA I 38 " pdb=" C5' DA I 38 " pdb=" C4' DA I 38 " ideal model delta sigma weight residual 109.40 113.17 -3.77 8.00e-01 1.56e+00 2.22e+01 ... (remaining 23266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 6997 16.55 - 33.09: 654 33.09 - 49.64: 930 49.64 - 66.19: 492 66.19 - 82.73: 11 Dihedral angle restraints: 9084 sinusoidal: 4597 harmonic: 4487 Sorted by residual: dihedral pdb=" CA CYS K 275 " pdb=" C CYS K 275 " pdb=" N ALA K 276 " pdb=" CA ALA K 276 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLU L 224 " pdb=" C GLU L 224 " pdb=" N VAL L 225 " pdb=" CA VAL L 225 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR N 236 " pdb=" C TYR N 236 " pdb=" N MET N 237 " pdb=" CA MET N 237 " ideal model delta harmonic sigma weight residual -180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1941 0.068 - 0.137: 642 0.137 - 0.205: 129 0.205 - 0.273: 22 0.273 - 0.341: 4 Chirality restraints: 2738 Sorted by residual: chirality pdb=" CA LYS A 116 " pdb=" N LYS A 116 " pdb=" C LYS A 116 " pdb=" CB LYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ARG M 248 " pdb=" N ARG M 248 " pdb=" C ARG M 248 " pdb=" CB ARG M 248 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA LYS F 78 " pdb=" N LYS F 78 " pdb=" C LYS F 78 " pdb=" CB LYS F 78 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2735 not shown) Planarity restraints: 2159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 121 " -0.042 2.00e-02 2.50e+03 1.70e-02 8.71e+00 pdb=" N9 DG J 121 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG J 121 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG J 121 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J 121 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 121 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 121 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DG J 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 121 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 121 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG J 121 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG J 121 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 79 " 0.037 2.00e-02 2.50e+03 1.56e-02 7.32e+00 pdb=" N9 DG J 79 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DG J 79 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG J 79 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG J 79 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 79 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 79 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG J 79 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG J 79 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J 79 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 79 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 79 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 130 " -0.037 2.00e-02 2.50e+03 1.55e-02 7.21e+00 pdb=" N9 DG J 130 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG J 130 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG J 130 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG J 130 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 130 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG J 130 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DG J 130 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 130 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG J 130 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 130 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG J 130 " 0.004 2.00e-02 2.50e+03 ... (remaining 2156 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 7236 2.99 - 3.47: 14532 3.47 - 3.94: 27132 3.94 - 4.42: 30898 4.42 - 4.90: 41898 Nonbonded interactions: 121696 Sorted by model distance: nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.509 3.040 nonbonded pdb=" OG1 THR H 91 " pdb=" OE1 GLU H 94 " model vdw 2.522 3.040 nonbonded pdb=" O3' DC J 78 " pdb=" C5' DG J 79 " model vdw 2.533 2.752 nonbonded pdb=" OG SER H 33 " pdb=" OP1 DG J 104 " model vdw 2.548 3.040 nonbonded pdb=" N SER D 88 " pdb=" OP1 DA I 40 " model vdw 2.564 3.120 ... (remaining 121691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 103) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.890 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16249 Z= 0.634 Angle : 1.009 8.061 23271 Z= 0.686 Chirality : 0.070 0.341 2738 Planarity : 0.006 0.048 2159 Dihedral : 24.600 82.733 6174 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.14 % Allowed : 1.88 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1535 helix: 0.33 (0.19), residues: 605 sheet: 0.79 (0.28), residues: 308 loop : 0.47 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 33 TYR 0.022 0.003 TYR D 43 PHE 0.021 0.003 PHE C 26 TRP 0.000 0.000 TRP K 146 HIS 0.012 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.63 (16249) covalent geometry : angle 1.00907 / 0.69 (23271) hydrogen bonds : bond 0.14922 / 9.96 ( 946) hydrogen bonds : angle 5.94500 / 4.37 ( 2387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.452 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: 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 63 ILE cc_start: 0.9511 (mt) cc_final: 0.9282 (mm) REVERT: A 66 LEU cc_start: 0.9862 (mt) cc_final: 0.9621 (tp) REVERT: A 68 PHE cc_start: 0.9665 (t80) cc_final: 0.9406 (t80) REVERT: A 74 GLU cc_start: 0.8792 (tt0) cc_final: 0.8074 (mt-10) REVERT: A 93 LEU cc_start: 0.9612 (mt) cc_final: 0.9404 (mt) REVERT: A 97 CYS cc_start: 0.9575 (m) cc_final: 0.9101 (m) REVERT: A 120 ILE cc_start: 0.9534 (pt) cc_final: 0.9269 (pt) REVERT: A 125 ILE cc_start: 0.9719 (mt) cc_final: 0.9418 (mp) REVERT: B 24 ARG cc_start: 0.8762 (mtm110) cc_final: 0.8304 (mpt180) REVERT: B 38 LEU cc_start: 0.9524 (mt) cc_final: 0.9213 (tt) REVERT: B 51 ILE cc_start: 0.9725 (mm) cc_final: 0.9272 (mm) REVERT: B 55 THR cc_start: 0.9793 (m) cc_final: 0.9319 (p) REVERT: B 63 LEU cc_start: 0.9721 (tp) cc_final: 0.9512 (mm) REVERT: B 79 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8158 (mtp180) REVERT: B 81 THR cc_start: 0.8843 (m) cc_final: 0.8581 (p) REVERT: C 39 ASN cc_start: 0.8725 (m-40) cc_final: 0.8375 (t0) REVERT: C 52 LEU cc_start: 0.9741 (tp) cc_final: 0.9489 (pp) REVERT: C 93 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9097 (tt0) REVERT: D 81 LEU cc_start: 0.9827 (mt) cc_final: 0.9625 (mp) REVERT: D 100 ARG cc_start: 0.9441 (mtp180) cc_final: 0.9154 (mtp85) REVERT: D 102 LEU cc_start: 0.8808 (mt) cc_final: 0.8528 (mt) REVERT: D 107 LEU cc_start: 0.9765 (mt) cc_final: 0.9273 (mt) REVERT: E 62 LEU cc_start: 0.8856 (mt) cc_final: 0.8577 (mt) REVERT: E 95 GLU cc_start: 0.9518 (mm-30) cc_final: 0.8845 (mm-30) REVERT: E 106 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9166 (tm-30) REVERT: E 110 LEU cc_start: 0.9669 (mt) cc_final: 0.9416 (mm) REVERT: F 45 LYS cc_start: 0.8823 (tttt) cc_final: 0.8549 (ttmt) REVERT: F 54 GLU cc_start: 0.9486 (tp30) cc_final: 0.8839 (tt0) REVERT: F 69 ASP cc_start: 0.9626 (m-30) cc_final: 0.9390 (m-30) REVERT: F 85 MET cc_start: 0.9261 (mmm) cc_final: 0.8906 (mmm) REVERT: F 97 THR cc_start: 0.9350 (m) cc_final: 0.8973 (t) REVERT: G 42 GLU cc_start: 0.9603 (tp30) cc_final: 0.9318 (tp30) REVERT: G 64 LEU cc_start: 0.9881 (mt) cc_final: 0.9656 (pp) REVERT: G 73 ASP cc_start: 0.9380 (m-30) cc_final: 0.9170 (m-30) REVERT: G 85 GLN cc_start: 0.9530 (tp-100) cc_final: 0.9259 (tp-100) REVERT: G 91 ASP cc_start: 0.9105 (t70) cc_final: 0.8805 (t0) REVERT: G 93 GLU cc_start: 0.9717 (mp0) cc_final: 0.9395 (mt-10) REVERT: G 95 ASN cc_start: 0.9540 (t0) cc_final: 0.9229 (m-40) REVERT: G 102 THR cc_start: 0.9640 (m) cc_final: 0.9406 (p) REVERT: H 57 SER cc_start: 0.9654 (m) cc_final: 0.9282 (p) REVERT: H 77 GLU cc_start: 0.9314 (tp30) cc_final: 0.8994 (tp30) REVERT: H 81 LEU cc_start: 0.9782 (mt) cc_final: 0.9444 (mp) REVERT: H 122 TYR cc_start: 0.9278 (t80) cc_final: 0.9024 (t80) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.1188 time to fit residues: 57.8477 Evaluate side-chains 231 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 94 GLN G 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.085192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052067 restraints weight = 83600.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053195 restraints weight = 49382.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053895 restraints weight = 34656.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054443 restraints weight = 27197.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.054791 restraints weight = 23050.974| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.227 16249 Z= 0.328 Angle : 0.880 11.391 23271 Z= 0.470 Chirality : 0.050 0.205 2738 Planarity : 0.006 0.048 2159 Dihedral : 28.296 70.718 4491 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.58 % Allowed : 3.62 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1535 helix: 0.66 (0.19), residues: 617 sheet: 0.78 (0.29), residues: 324 loop : 0.37 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 93 TYR 0.027 0.003 TYR D 84 PHE 0.019 0.003 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.013 0.003 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.33 (16249) covalent geometry : angle 0.88045 / 0.47 (23271) hydrogen bonds : bond 0.10822 / 7.29 ( 946) hydrogen bonds : angle 4.81637 / 3.52 ( 2387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 240 time to evaluate : 0.395 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: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9771 (t80) cc_final: 0.9432 (t80) REVERT: A 74 GLU cc_start: 0.8767 (tt0) cc_final: 0.8052 (mt-10) REVERT: A 86 GLN cc_start: 0.9225 (mt0) cc_final: 0.8799 (mt0) REVERT: A 95 GLU cc_start: 0.9569 (tp30) cc_final: 0.9288 (tp30) REVERT: A 97 CYS cc_start: 0.9677 (m) cc_final: 0.9444 (m) REVERT: A 98 GLU cc_start: 0.9412 (mt-10) cc_final: 0.8821 (mt-10) REVERT: A 106 GLU cc_start: 0.9710 (tt0) cc_final: 0.9507 (tm-30) REVERT: A 121 MET cc_start: 0.8544 (mmp) cc_final: 0.8228 (mmm) REVERT: B 24 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8068 (mmt180) REVERT: B 51 ILE cc_start: 0.9421 (mm) cc_final: 0.9179 (mm) REVERT: B 55 THR cc_start: 0.9641 (m) cc_final: 0.9353 (m) REVERT: B 69 ASP cc_start: 0.9670 (m-30) cc_final: 0.9436 (m-30) REVERT: B 92 LYS cc_start: 0.9169 (pttt) cc_final: 0.8697 (pttt) REVERT: C 39 ASN cc_start: 0.8677 (m-40) cc_final: 0.8185 (t0) REVERT: C 116 LEU cc_start: 0.9393 (mm) cc_final: 0.8730 (mm) REVERT: D 60 MET cc_start: 0.9239 (tpp) cc_final: 0.9030 (tpp) REVERT: D 85 ASN cc_start: 0.9412 (m110) cc_final: 0.9039 (m-40) REVERT: D 100 ARG cc_start: 0.9519 (mtp180) cc_final: 0.9082 (mtp180) REVERT: E 56 GLN cc_start: 0.9385 (mt0) cc_final: 0.9018 (pt0) REVERT: E 69 GLN cc_start: 0.9709 (mm-40) cc_final: 0.9494 (mm-40) REVERT: E 91 MET cc_start: 0.9562 (mmp) cc_final: 0.9037 (mmm) REVERT: E 106 GLU cc_start: 0.9621 (mt-10) cc_final: 0.9253 (tm-30) REVERT: E 110 LEU cc_start: 0.9695 (mt) cc_final: 0.9432 (mm) REVERT: E 121 MET cc_start: 0.8620 (ttm) cc_final: 0.8303 (ttm) REVERT: F 38 LEU cc_start: 0.9841 (mm) cc_final: 0.9640 (mm) REVERT: F 54 GLU cc_start: 0.9588 (tp30) cc_final: 0.8982 (tt0) REVERT: F 85 MET cc_start: 0.9295 (mmm) cc_final: 0.8840 (mmm) REVERT: F 86 ASP cc_start: 0.8663 (m-30) cc_final: 0.8070 (t70) REVERT: F 97 THR cc_start: 0.9454 (m) cc_final: 0.9231 (t) REVERT: G 26 PHE cc_start: 0.9077 (m-10) cc_final: 0.8287 (m-10) REVERT: G 42 GLU cc_start: 0.9356 (tp30) cc_final: 0.9135 (tp30) REVERT: G 73 ASP cc_start: 0.9239 (m-30) cc_final: 0.9021 (m-30) REVERT: G 91 ASP cc_start: 0.9185 (t70) cc_final: 0.8937 (t70) REVERT: G 93 GLU cc_start: 0.9713 (mp0) cc_final: 0.9356 (tt0) REVERT: G 95 ASN cc_start: 0.9627 (t0) cc_final: 0.9375 (m-40) REVERT: G 97 LEU cc_start: 0.9543 (mt) cc_final: 0.9258 (mt) REVERT: G 105 GLN cc_start: 0.9409 (mp10) cc_final: 0.8842 (mp10) REVERT: H 57 SER cc_start: 0.9552 (m) cc_final: 0.9215 (p) REVERT: H 102 LEU cc_start: 0.9030 (mp) cc_final: 0.8822 (mp) outliers start: 4 outliers final: 2 residues processed: 243 average time/residue: 0.0841 time to fit residues: 32.1538 Evaluate side-chains 204 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 40.0000 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 105 optimal weight: 50.0000 chunk 138 optimal weight: 7.9990 chunk 127 optimal weight: 0.2980 chunk 94 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.3930 r_free = 0.3930 target = 0.088277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.053919 restraints weight = 84272.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.055128 restraints weight = 47176.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055950 restraints weight = 32233.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056467 restraints weight = 24668.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056774 restraints weight = 20651.196| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16249 Z= 0.177 Angle : 0.645 9.076 23271 Z= 0.361 Chirality : 0.043 0.191 2738 Planarity : 0.005 0.043 2159 Dihedral : 27.706 77.518 4491 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.29 % Allowed : 2.17 % Favored : 97.54 % 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: 1.23 (0.21), residues: 1535 helix: 1.37 (0.20), residues: 616 sheet: 0.84 (0.29), residues: 324 loop : 0.37 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 93 TYR 0.018 0.002 TYR A 100 PHE 0.018 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.015 0.003 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (16249) covalent geometry : angle 0.64532 / 0.36 (23271) hydrogen bonds : bond 0.05985 / 3.96 ( 946) hydrogen bonds : angle 4.08636 / 2.98 ( 2387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 0.517 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: symmetry clash REVERT: A 61 LEU cc_start: 0.8812 (mt) cc_final: 0.8594 (mt) REVERT: A 63 ILE cc_start: 0.9473 (mm) cc_final: 0.9217 (mm) REVERT: A 68 PHE cc_start: 0.9747 (t80) cc_final: 0.9397 (t80) REVERT: A 74 GLU cc_start: 0.8675 (tt0) cc_final: 0.7935 (tt0) REVERT: A 86 GLN cc_start: 0.9316 (mt0) cc_final: 0.8904 (mt0) REVERT: A 97 CYS cc_start: 0.9622 (m) cc_final: 0.9399 (m) REVERT: A 98 GLU cc_start: 0.9454 (mt-10) cc_final: 0.8745 (mt-10) REVERT: A 106 GLU cc_start: 0.9690 (tt0) cc_final: 0.9481 (tm-30) REVERT: A 121 MET cc_start: 0.8695 (mmp) cc_final: 0.8242 (mmm) REVERT: B 24 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8108 (mpt180) REVERT: B 79 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8432 (mtm180) REVERT: B 86 ASP cc_start: 0.9294 (m-30) cc_final: 0.8945 (m-30) REVERT: C 26 PHE cc_start: 0.8621 (m-10) cc_final: 0.8321 (m-10) REVERT: C 39 ASN cc_start: 0.8711 (m-40) cc_final: 0.8406 (t0) REVERT: C 84 LEU cc_start: 0.9707 (mp) cc_final: 0.9500 (mp) REVERT: C 88 ILE cc_start: 0.9588 (mt) cc_final: 0.9375 (tp) REVERT: D 90 ILE cc_start: 0.9100 (mm) cc_final: 0.8898 (mm) REVERT: D 94 GLU cc_start: 0.9596 (mp0) cc_final: 0.9226 (mp0) REVERT: D 100 ARG cc_start: 0.9449 (mtp180) cc_final: 0.8958 (mtp180) REVERT: D 103 LEU cc_start: 0.9635 (mt) cc_final: 0.9415 (tp) REVERT: E 47 VAL cc_start: 0.8976 (t) cc_final: 0.8082 (t) REVERT: E 56 GLN cc_start: 0.9398 (mt0) cc_final: 0.8917 (pt0) REVERT: E 69 GLN cc_start: 0.9691 (mm-40) cc_final: 0.9487 (mm110) REVERT: E 86 GLN cc_start: 0.9220 (mt0) cc_final: 0.8859 (mt0) REVERT: E 91 MET cc_start: 0.9487 (mmp) cc_final: 0.8942 (mmm) REVERT: E 95 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9098 (mm-30) REVERT: E 106 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9265 (tm-30) REVERT: E 121 MET cc_start: 0.8353 (ttm) cc_final: 0.7810 (ttm) REVERT: E 127 LEU cc_start: 0.9681 (mm) cc_final: 0.9461 (tt) REVERT: F 38 LEU cc_start: 0.9795 (mm) cc_final: 0.9551 (mm) REVERT: F 54 GLU cc_start: 0.9547 (tp30) cc_final: 0.9051 (tt0) REVERT: F 59 LEU cc_start: 0.9680 (mm) cc_final: 0.9463 (mm) REVERT: F 85 MET cc_start: 0.9231 (mmm) cc_final: 0.8650 (mmm) REVERT: F 86 ASP cc_start: 0.8682 (m-30) cc_final: 0.8334 (t70) REVERT: F 97 THR cc_start: 0.9422 (m) cc_final: 0.9196 (t) REVERT: G 26 PHE cc_start: 0.8873 (m-10) cc_final: 0.8109 (m-10) REVERT: G 42 GLU cc_start: 0.9347 (tp30) cc_final: 0.9089 (tp30) REVERT: G 57 GLU cc_start: 0.9266 (pm20) cc_final: 0.8991 (pm20) REVERT: G 73 ASP cc_start: 0.9175 (m-30) cc_final: 0.8940 (m-30) REVERT: G 88 ILE cc_start: 0.9506 (tt) cc_final: 0.9270 (tp) REVERT: G 91 ASP cc_start: 0.9214 (t70) cc_final: 0.8757 (t70) REVERT: G 93 GLU cc_start: 0.9637 (mp0) cc_final: 0.9323 (tt0) REVERT: G 95 ASN cc_start: 0.9606 (t0) cc_final: 0.9363 (m-40) REVERT: G 97 LEU cc_start: 0.9539 (mt) cc_final: 0.9301 (mt) REVERT: G 105 GLN cc_start: 0.9400 (mp10) cc_final: 0.8804 (mp10) REVERT: H 38 TYR cc_start: 0.9200 (m-80) cc_final: 0.8863 (m-10) REVERT: H 57 SER cc_start: 0.9525 (m) cc_final: 0.9247 (p) REVERT: H 101 LEU cc_start: 0.9515 (tp) cc_final: 0.9110 (tp) REVERT: H 122 TYR cc_start: 0.9298 (t80) cc_final: 0.9024 (t80) outliers start: 2 outliers final: 1 residues processed: 255 average time/residue: 0.1032 time to fit residues: 41.5502 Evaluate side-chains 209 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 80 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 105 optimal weight: 5.9990 chunk 101 optimal weight: 50.0000 chunk 174 optimal weight: 50.0000 chunk 92 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.050455 restraints weight = 84953.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051452 restraints weight = 50251.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.052122 restraints weight = 35516.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.052591 restraints weight = 27972.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052935 restraints weight = 23991.463| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.202 16249 Z= 0.292 Angle : 0.735 10.854 23271 Z= 0.415 Chirality : 0.044 0.185 2738 Planarity : 0.005 0.059 2159 Dihedral : 27.569 75.947 4491 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1535 helix: 0.84 (0.19), residues: 614 sheet: 0.82 (0.29), residues: 324 loop : 0.33 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 36 TYR 0.024 0.002 TYR H 84 PHE 0.015 0.002 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.013 0.003 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.29 (16249) covalent geometry : angle 0.73493 / 0.42 (23271) hydrogen bonds : bond 0.09984 / 6.73 ( 946) hydrogen bonds : angle 4.48167 / 3.24 ( 2387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.524 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 74 GLU cc_start: 0.8767 (tt0) cc_final: 0.8122 (tt0) REVERT: A 86 GLN cc_start: 0.9292 (mt0) cc_final: 0.8880 (mt0) REVERT: A 97 CYS cc_start: 0.9686 (m) cc_final: 0.9418 (m) REVERT: A 106 GLU cc_start: 0.9713 (tt0) cc_final: 0.9456 (tm-30) REVERT: A 121 MET cc_start: 0.8864 (mmp) cc_final: 0.8513 (mmm) REVERT: B 61 VAL cc_start: 0.9704 (m) cc_final: 0.9452 (m) REVERT: B 82 VAL cc_start: 0.9510 (t) cc_final: 0.9297 (t) REVERT: B 86 ASP cc_start: 0.9194 (m-30) cc_final: 0.8926 (t0) REVERT: C 26 PHE cc_start: 0.8799 (m-10) cc_final: 0.8311 (m-10) REVERT: C 39 ASN cc_start: 0.8976 (m-40) cc_final: 0.8620 (m-40) REVERT: C 116 LEU cc_start: 0.9381 (mm) cc_final: 0.8818 (tt) REVERT: D 87 ARG cc_start: 0.9569 (mmt-90) cc_final: 0.9162 (mmp80) REVERT: D 100 ARG cc_start: 0.9434 (mtp180) cc_final: 0.9052 (mmm-85) REVERT: D 103 LEU cc_start: 0.9687 (mt) cc_final: 0.9437 (tp) REVERT: D 106 GLU cc_start: 0.8871 (pm20) cc_final: 0.8395 (pm20) REVERT: D 107 LEU cc_start: 0.9720 (mm) cc_final: 0.9468 (mm) REVERT: E 52 ILE cc_start: 0.9001 (mm) cc_final: 0.8755 (mm) REVERT: E 56 GLN cc_start: 0.9534 (mt0) cc_final: 0.9102 (pt0) REVERT: E 69 GLN cc_start: 0.9701 (mm-40) cc_final: 0.9457 (mm110) REVERT: E 91 MET cc_start: 0.9512 (mmp) cc_final: 0.9285 (mmm) REVERT: E 106 GLU cc_start: 0.9600 (mt-10) cc_final: 0.9321 (tm-30) REVERT: F 38 LEU cc_start: 0.9834 (mm) cc_final: 0.9584 (mm) REVERT: F 54 GLU cc_start: 0.9558 (tp30) cc_final: 0.9083 (tt0) REVERT: F 85 MET cc_start: 0.9361 (mmm) cc_final: 0.8974 (mmm) REVERT: F 86 ASP cc_start: 0.8933 (m-30) cc_final: 0.8503 (t70) REVERT: F 97 THR cc_start: 0.9423 (m) cc_final: 0.9168 (t) REVERT: G 26 PHE cc_start: 0.9154 (m-10) cc_final: 0.8741 (m-10) REVERT: G 39 ASN cc_start: 0.9040 (m-40) cc_final: 0.8415 (t0) REVERT: G 73 ASP cc_start: 0.9228 (m-30) cc_final: 0.9026 (m-30) REVERT: G 91 ASP cc_start: 0.9176 (t70) cc_final: 0.8868 (t70) REVERT: G 93 GLU cc_start: 0.9653 (mp0) cc_final: 0.9396 (mt-10) REVERT: G 97 LEU cc_start: 0.9534 (mt) cc_final: 0.9267 (mt) REVERT: G 105 GLN cc_start: 0.9424 (mp10) cc_final: 0.8846 (mp10) REVERT: H 57 SER cc_start: 0.9527 (m) cc_final: 0.9245 (p) REVERT: H 68 ASN cc_start: 0.9483 (m110) cc_final: 0.8971 (t0) REVERT: H 95 ILE cc_start: 0.9793 (mt) cc_final: 0.9519 (tt) REVERT: H 107 LEU cc_start: 0.9623 (mt) cc_final: 0.9414 (mt) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.0998 time to fit residues: 35.8354 Evaluate side-chains 188 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 93 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 154 optimal weight: 50.0000 chunk 156 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 129 optimal weight: 0.0270 chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 50.0000 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** F 76 HIS ** 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 = 0.3919 r_free = 0.3919 target = 0.087423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053424 restraints weight = 83352.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.054343 restraints weight = 47001.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055110 restraints weight = 31908.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.055680 restraints weight = 24664.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.056092 restraints weight = 20606.238| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16249 Z= 0.160 Angle : 0.638 14.402 23271 Z= 0.359 Chirality : 0.044 0.300 2738 Planarity : 0.005 0.096 2159 Dihedral : 27.512 78.827 4491 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 1.35 (0.21), residues: 1535 helix: 1.49 (0.20), residues: 614 sheet: 0.89 (0.29), residues: 324 loop : 0.43 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 18 TYR 0.021 0.002 TYR A 100 PHE 0.020 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.014 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (16249) covalent geometry : angle 0.63828 / 0.36 (23271) hydrogen bonds : bond 0.05043 / 3.38 ( 946) hydrogen bonds : angle 3.93256 / 2.87 ( 2387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.516 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: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8674 (mt) cc_final: 0.8398 (mt) REVERT: A 68 PHE cc_start: 0.9841 (t80) cc_final: 0.9446 (t80) REVERT: A 74 GLU cc_start: 0.8715 (tt0) cc_final: 0.8139 (mt-10) REVERT: A 97 CYS cc_start: 0.9667 (m) cc_final: 0.9379 (p) REVERT: A 121 MET cc_start: 0.8760 (mmp) cc_final: 0.8176 (mmm) REVERT: B 61 VAL cc_start: 0.9740 (m) cc_final: 0.9442 (m) REVERT: B 86 ASP cc_start: 0.9216 (m-30) cc_final: 0.8875 (t70) REVERT: C 26 PHE cc_start: 0.8697 (m-10) cc_final: 0.8136 (m-10) REVERT: C 39 ASN cc_start: 0.8840 (m-40) cc_final: 0.8473 (m-40) REVERT: D 102 LEU cc_start: 0.9378 (mm) cc_final: 0.9072 (mm) REVERT: D 103 LEU cc_start: 0.9610 (mt) cc_final: 0.9309 (tp) REVERT: D 106 GLU cc_start: 0.9021 (pm20) cc_final: 0.8655 (pm20) REVERT: D 107 LEU cc_start: 0.9731 (mm) cc_final: 0.9229 (mm) REVERT: E 52 ILE cc_start: 0.8927 (mm) cc_final: 0.8568 (mm) REVERT: E 56 GLN cc_start: 0.9484 (mt0) cc_final: 0.8971 (pt0) REVERT: E 69 GLN cc_start: 0.9664 (mm-40) cc_final: 0.9438 (mm110) REVERT: E 91 MET cc_start: 0.9449 (mmp) cc_final: 0.9196 (mmp) REVERT: E 95 GLU cc_start: 0.9721 (mm-30) cc_final: 0.9231 (mm-30) REVERT: E 106 GLU cc_start: 0.9553 (mt-10) cc_final: 0.9311 (tm-30) REVERT: E 121 MET cc_start: 0.8753 (tpp) cc_final: 0.8387 (tpt) REVERT: F 54 GLU cc_start: 0.9530 (tp30) cc_final: 0.9094 (tt0) REVERT: F 85 MET cc_start: 0.9335 (mmm) cc_final: 0.8989 (mmp) REVERT: F 86 ASP cc_start: 0.8897 (m-30) cc_final: 0.8469 (t70) REVERT: F 97 THR cc_start: 0.9427 (m) cc_final: 0.9172 (t) REVERT: G 26 PHE cc_start: 0.9125 (m-10) cc_final: 0.8827 (m-10) REVERT: G 39 ASN cc_start: 0.9101 (m-40) cc_final: 0.8440 (t0) REVERT: G 64 LEU cc_start: 0.9824 (mt) cc_final: 0.9565 (pp) REVERT: G 65 GLU cc_start: 0.9535 (tm-30) cc_final: 0.9306 (tm-30) REVERT: G 73 ASP cc_start: 0.9193 (m-30) cc_final: 0.8983 (m-30) REVERT: G 91 ASP cc_start: 0.9192 (t70) cc_final: 0.8757 (t70) REVERT: G 93 GLU cc_start: 0.9660 (mp0) cc_final: 0.9228 (tt0) REVERT: G 96 LYS cc_start: 0.9639 (mmtp) cc_final: 0.9437 (mmmm) REVERT: G 97 LEU cc_start: 0.9527 (mt) cc_final: 0.9258 (mt) REVERT: G 105 GLN cc_start: 0.9385 (mp10) cc_final: 0.8875 (mp10) REVERT: H 57 SER cc_start: 0.9430 (m) cc_final: 0.9156 (p) REVERT: H 68 ASN cc_start: 0.9465 (m110) cc_final: 0.8904 (t0) REVERT: H 95 ILE cc_start: 0.9786 (mt) cc_final: 0.9482 (tt) REVERT: H 107 LEU cc_start: 0.9626 (mt) cc_final: 0.9027 (mt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0991 time to fit residues: 38.5429 Evaluate side-chains 202 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 129 optimal weight: 50.0000 chunk 160 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.3889 r_free = 0.3889 target = 0.085231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.051508 restraints weight = 84281.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.052649 restraints weight = 47865.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053351 restraints weight = 33204.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053761 restraints weight = 25676.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054177 restraints weight = 21876.467| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 16249 Z= 0.210 Angle : 0.660 12.368 23271 Z= 0.372 Chirality : 0.042 0.282 2738 Planarity : 0.005 0.053 2159 Dihedral : 27.385 79.306 4491 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 1.30 (0.21), residues: 1535 helix: 1.44 (0.20), residues: 608 sheet: 0.71 (0.29), residues: 340 loop : 0.51 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 18 TYR 0.012 0.002 TYR C 58 PHE 0.019 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.012 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (16249) covalent geometry : angle 0.66032 / 0.37 (23271) hydrogen bonds : bond 0.06840 / 4.62 ( 946) hydrogen bonds : angle 4.05903 / 2.95 ( 2387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.515 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: A 61 LEU cc_start: 0.8601 (mt) cc_final: 0.8327 (mt) REVERT: A 68 PHE cc_start: 0.9832 (t80) cc_final: 0.9561 (t80) REVERT: A 74 GLU cc_start: 0.8748 (tt0) cc_final: 0.8091 (tt0) REVERT: A 83 LEU cc_start: 0.9278 (tp) cc_final: 0.8920 (mt) REVERT: A 97 CYS cc_start: 0.9641 (m) cc_final: 0.9326 (p) REVERT: A 106 GLU cc_start: 0.9688 (tt0) cc_final: 0.9394 (tm-30) REVERT: A 121 MET cc_start: 0.8880 (mmp) cc_final: 0.8208 (mmm) REVERT: B 51 ILE cc_start: 0.9404 (mm) cc_final: 0.8636 (mm) REVERT: B 61 VAL cc_start: 0.9752 (m) cc_final: 0.9453 (m) REVERT: B 69 ASP cc_start: 0.9537 (m-30) cc_final: 0.9292 (m-30) REVERT: B 82 VAL cc_start: 0.9485 (t) cc_final: 0.9208 (t) REVERT: B 86 ASP cc_start: 0.9184 (m-30) cc_final: 0.8912 (t70) REVERT: C 39 ASN cc_start: 0.8850 (m-40) cc_final: 0.8474 (m-40) REVERT: D 81 LEU cc_start: 0.9778 (tt) cc_final: 0.9534 (tt) REVERT: D 85 ASN cc_start: 0.9134 (m110) cc_final: 0.8789 (p0) REVERT: D 100 ARG cc_start: 0.9303 (mtp180) cc_final: 0.9018 (mtp85) REVERT: D 102 LEU cc_start: 0.9463 (mm) cc_final: 0.8940 (mm) REVERT: D 103 LEU cc_start: 0.9584 (mt) cc_final: 0.9313 (tp) REVERT: D 106 GLU cc_start: 0.9061 (pm20) cc_final: 0.8744 (pm20) REVERT: D 107 LEU cc_start: 0.9698 (mm) cc_final: 0.9194 (mm) REVERT: E 52 ILE cc_start: 0.8951 (mm) cc_final: 0.8594 (mm) REVERT: E 56 GLN cc_start: 0.9489 (mt0) cc_final: 0.8962 (pt0) REVERT: E 91 MET cc_start: 0.9457 (mmp) cc_final: 0.9243 (mmm) REVERT: E 106 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9320 (tm-30) REVERT: E 121 MET cc_start: 0.8841 (tpp) cc_final: 0.8379 (tpt) REVERT: F 38 LEU cc_start: 0.9778 (mm) cc_final: 0.9575 (mm) REVERT: F 45 LYS cc_start: 0.9094 (ptpt) cc_final: 0.8860 (ptpt) REVERT: F 54 GLU cc_start: 0.9495 (tp30) cc_final: 0.9147 (tt0) REVERT: F 59 LEU cc_start: 0.9689 (mm) cc_final: 0.9478 (mm) REVERT: F 85 MET cc_start: 0.9299 (mmm) cc_final: 0.9003 (mmp) REVERT: F 86 ASP cc_start: 0.8880 (m-30) cc_final: 0.8466 (t70) REVERT: F 97 THR cc_start: 0.9468 (m) cc_final: 0.9117 (p) REVERT: G 26 PHE cc_start: 0.9100 (m-10) cc_final: 0.8849 (m-10) REVERT: G 39 ASN cc_start: 0.9061 (m-40) cc_final: 0.8486 (t0) REVERT: G 64 LEU cc_start: 0.9823 (mt) cc_final: 0.9591 (pp) REVERT: G 65 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9283 (tm-30) REVERT: G 91 ASP cc_start: 0.9195 (t70) cc_final: 0.8565 (t70) REVERT: G 93 GLU cc_start: 0.9672 (mp0) cc_final: 0.9363 (pm20) REVERT: G 96 LYS cc_start: 0.9646 (mmtp) cc_final: 0.9432 (mmmm) REVERT: G 97 LEU cc_start: 0.9530 (mt) cc_final: 0.9203 (mt) REVERT: G 105 GLN cc_start: 0.9413 (mp10) cc_final: 0.8879 (mp10) REVERT: H 57 SER cc_start: 0.9469 (m) cc_final: 0.9203 (p) REVERT: H 68 ASN cc_start: 0.9486 (m110) cc_final: 0.8888 (t0) REVERT: H 95 ILE cc_start: 0.9787 (mt) cc_final: 0.9547 (tt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1004 time to fit residues: 36.8285 Evaluate side-chains 191 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 111 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 86 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.3895 r_free = 0.3895 target = 0.085596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.052199 restraints weight = 83059.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.053362 restraints weight = 47586.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.054165 restraints weight = 32797.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.054693 restraints weight = 25358.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.055048 restraints weight = 21355.618| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 16249 Z= 0.182 Angle : 0.636 13.112 23271 Z= 0.362 Chirality : 0.043 0.292 2738 Planarity : 0.004 0.049 2159 Dihedral : 27.359 80.785 4491 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 1.46 (0.21), residues: 1535 helix: 1.57 (0.20), residues: 608 sheet: 0.79 (0.29), residues: 340 loop : 0.60 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 18 TYR 0.019 0.002 TYR H 41 PHE 0.022 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (16249) covalent geometry : angle 0.63594 / 0.36 (23271) hydrogen bonds : bond 0.05591 / 3.76 ( 946) hydrogen bonds : angle 3.98248 / 2.89 ( 2387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.462 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: A 52 ILE cc_start: 0.9251 (mm) cc_final: 0.9008 (mm) REVERT: A 61 LEU cc_start: 0.8549 (mt) cc_final: 0.8172 (mt) REVERT: A 68 PHE cc_start: 0.9843 (t80) cc_final: 0.9565 (t80) REVERT: A 74 GLU cc_start: 0.8689 (tt0) cc_final: 0.8026 (tt0) REVERT: A 78 ASP cc_start: 0.9622 (m-30) cc_final: 0.9212 (m-30) REVERT: A 82 ASP cc_start: 0.9154 (m-30) cc_final: 0.8678 (p0) REVERT: A 83 LEU cc_start: 0.9326 (tp) cc_final: 0.8865 (mt) REVERT: A 97 CYS cc_start: 0.9654 (m) cc_final: 0.9328 (p) REVERT: A 106 GLU cc_start: 0.9699 (tt0) cc_final: 0.9393 (tm-30) REVERT: A 121 MET cc_start: 0.8786 (mmp) cc_final: 0.8242 (mmm) REVERT: B 61 VAL cc_start: 0.9749 (m) cc_final: 0.9470 (m) REVERT: C 26 PHE cc_start: 0.8633 (m-10) cc_final: 0.8240 (m-10) REVERT: C 39 ASN cc_start: 0.8889 (m-40) cc_final: 0.8356 (m-40) REVERT: D 60 MET cc_start: 0.9311 (tpp) cc_final: 0.9012 (tpp) REVERT: D 81 LEU cc_start: 0.9789 (tt) cc_final: 0.9569 (tt) REVERT: D 85 ASN cc_start: 0.9056 (m110) cc_final: 0.8677 (p0) REVERT: D 87 ARG cc_start: 0.9528 (mmt-90) cc_final: 0.9228 (mmm160) REVERT: D 90 ILE cc_start: 0.8829 (mm) cc_final: 0.8595 (mm) REVERT: D 100 ARG cc_start: 0.9226 (mtp180) cc_final: 0.8909 (mmm-85) REVERT: D 102 LEU cc_start: 0.9416 (mm) cc_final: 0.9088 (mm) REVERT: D 103 LEU cc_start: 0.9486 (mt) cc_final: 0.9183 (tp) REVERT: D 106 GLU cc_start: 0.9098 (pm20) cc_final: 0.8769 (pm20) REVERT: D 107 LEU cc_start: 0.9710 (mm) cc_final: 0.9226 (mm) REVERT: E 51 GLU cc_start: 0.9451 (mp0) cc_final: 0.9148 (mp0) REVERT: E 52 ILE cc_start: 0.9009 (mm) cc_final: 0.8518 (mm) REVERT: E 69 GLN cc_start: 0.9453 (mp-120) cc_final: 0.9231 (mp10) REVERT: E 95 GLU cc_start: 0.9725 (mm-30) cc_final: 0.9115 (tp30) REVERT: E 106 GLU cc_start: 0.9535 (mt-10) cc_final: 0.9269 (tm-30) REVERT: E 121 MET cc_start: 0.8770 (tpp) cc_final: 0.8343 (tpt) REVERT: F 38 LEU cc_start: 0.9785 (mm) cc_final: 0.9549 (mm) REVERT: F 45 LYS cc_start: 0.9085 (ptpt) cc_final: 0.8822 (ptpt) REVERT: F 54 GLU cc_start: 0.9514 (tp30) cc_final: 0.9135 (tt0) REVERT: F 59 LEU cc_start: 0.9677 (mm) cc_final: 0.9455 (mm) REVERT: F 85 MET cc_start: 0.9364 (mmm) cc_final: 0.8938 (mmm) REVERT: F 86 ASP cc_start: 0.8989 (m-30) cc_final: 0.8524 (t70) REVERT: F 97 THR cc_start: 0.9427 (m) cc_final: 0.9071 (p) REVERT: G 26 PHE cc_start: 0.9096 (m-10) cc_final: 0.8770 (m-10) REVERT: G 39 ASN cc_start: 0.9153 (m-40) cc_final: 0.8520 (t0) REVERT: G 64 LEU cc_start: 0.9827 (mt) cc_final: 0.9571 (pp) REVERT: G 91 ASP cc_start: 0.9260 (t70) cc_final: 0.8571 (t70) REVERT: G 93 GLU cc_start: 0.9662 (mp0) cc_final: 0.9360 (pm20) REVERT: G 94 LEU cc_start: 0.9746 (mp) cc_final: 0.9466 (mt) REVERT: G 96 LYS cc_start: 0.9631 (mmtp) cc_final: 0.9396 (mmmm) REVERT: G 105 GLN cc_start: 0.9415 (mp10) cc_final: 0.8875 (mp10) REVERT: H 68 ASN cc_start: 0.9471 (m110) cc_final: 0.8897 (t0) REVERT: H 95 ILE cc_start: 0.9771 (mt) cc_final: 0.9514 (tt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0977 time to fit residues: 35.8232 Evaluate side-chains 192 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.083667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.050797 restraints weight = 85474.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.051855 restraints weight = 50832.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.052574 restraints weight = 35907.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053084 restraints weight = 28205.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.053396 restraints weight = 23663.981| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 16249 Z= 0.225 Angle : 0.662 11.823 23271 Z= 0.379 Chirality : 0.042 0.285 2738 Planarity : 0.005 0.046 2159 Dihedral : 27.364 81.926 4491 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 1.37 (0.21), residues: 1535 helix: 1.43 (0.20), residues: 609 sheet: 0.81 (0.29), residues: 340 loop : 0.60 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 18 TYR 0.048 0.003 TYR H 84 PHE 0.009 0.002 PHE E 79 TRP 0.000 0.000 TRP K 146 HIS 0.011 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.23 (16249) covalent geometry : angle 0.66156 / 0.38 (23271) hydrogen bonds : bond 0.07437 / 5.04 ( 946) hydrogen bonds : angle 4.15211 / 3.00 ( 2387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.9286 (mm) cc_final: 0.9030 (mm) REVERT: A 68 PHE cc_start: 0.9822 (t80) cc_final: 0.9572 (t80) REVERT: A 74 GLU cc_start: 0.8771 (tt0) cc_final: 0.8135 (tt0) REVERT: A 82 ASP cc_start: 0.9172 (m-30) cc_final: 0.8626 (p0) REVERT: A 97 CYS cc_start: 0.9656 (m) cc_final: 0.9348 (p) REVERT: A 106 GLU cc_start: 0.9696 (tt0) cc_final: 0.9380 (tm-30) REVERT: A 121 MET cc_start: 0.8871 (mmp) cc_final: 0.8294 (mmm) REVERT: C 26 PHE cc_start: 0.8640 (m-10) cc_final: 0.8123 (m-80) REVERT: D 77 GLU cc_start: 0.9413 (tp30) cc_final: 0.9197 (tp30) REVERT: D 85 ASN cc_start: 0.9058 (m110) cc_final: 0.8664 (p0) REVERT: D 87 ARG cc_start: 0.9567 (mmt-90) cc_final: 0.9283 (mmm160) REVERT: D 90 ILE cc_start: 0.8831 (mm) cc_final: 0.8611 (mm) REVERT: D 100 ARG cc_start: 0.9292 (mtp180) cc_final: 0.8955 (mmm-85) REVERT: D 102 LEU cc_start: 0.9477 (mm) cc_final: 0.9110 (mm) REVERT: D 103 LEU cc_start: 0.9548 (mt) cc_final: 0.9249 (tp) REVERT: D 106 GLU cc_start: 0.9175 (pm20) cc_final: 0.8776 (pm20) REVERT: D 107 LEU cc_start: 0.9732 (mm) cc_final: 0.9466 (mm) REVERT: E 106 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9263 (tm-30) REVERT: E 121 MET cc_start: 0.8926 (tpp) cc_final: 0.8379 (tpt) REVERT: F 38 LEU cc_start: 0.9780 (mm) cc_final: 0.9576 (mm) REVERT: F 45 LYS cc_start: 0.9055 (ptpt) cc_final: 0.8786 (ptpt) REVERT: F 54 GLU cc_start: 0.9521 (tp30) cc_final: 0.9173 (tt0) REVERT: F 59 LEU cc_start: 0.9698 (mm) cc_final: 0.9476 (mm) REVERT: F 69 ASP cc_start: 0.9581 (m-30) cc_final: 0.9336 (m-30) REVERT: F 85 MET cc_start: 0.9236 (mmm) cc_final: 0.8797 (mmp) REVERT: F 86 ASP cc_start: 0.8968 (m-30) cc_final: 0.8522 (t0) REVERT: F 97 THR cc_start: 0.9402 (m) cc_final: 0.9028 (p) REVERT: G 26 PHE cc_start: 0.9118 (m-10) cc_final: 0.8884 (m-10) REVERT: G 64 LEU cc_start: 0.9829 (mt) cc_final: 0.9579 (pp) REVERT: G 91 ASP cc_start: 0.9257 (t70) cc_final: 0.8640 (t70) REVERT: G 93 GLU cc_start: 0.9684 (mp0) cc_final: 0.9378 (pm20) REVERT: G 94 LEU cc_start: 0.9762 (mp) cc_final: 0.9503 (mt) REVERT: G 96 LYS cc_start: 0.9640 (mmtp) cc_final: 0.9399 (mmmm) REVERT: G 105 GLN cc_start: 0.9396 (mp10) cc_final: 0.8878 (mp10) REVERT: H 68 ASN cc_start: 0.9478 (m110) cc_final: 0.8887 (t0) REVERT: H 95 ILE cc_start: 0.9773 (mt) cc_final: 0.9542 (tt) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1012 time to fit residues: 34.8659 Evaluate side-chains 178 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 0.0970 chunk 141 optimal weight: 50.0000 chunk 161 optimal weight: 0.0970 chunk 105 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 129 optimal weight: 50.0000 chunk 69 optimal weight: 0.8980 chunk 106 optimal weight: 40.0000 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.090345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.055265 restraints weight = 81988.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.056200 restraints weight = 49910.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056726 restraints weight = 35350.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.057286 restraints weight = 28274.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.057533 restraints weight = 24176.254| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 16249 Z= 0.140 Angle : 0.612 14.294 23271 Z= 0.346 Chirality : 0.043 0.290 2738 Planarity : 0.004 0.053 2159 Dihedral : 27.274 81.764 4491 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 1.55 (0.21), residues: 1535 helix: 1.66 (0.20), residues: 610 sheet: 0.81 (0.29), residues: 340 loop : 0.65 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 18 TYR 0.031 0.002 TYR F 89 PHE 0.026 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (16249) covalent geometry : angle 0.61242 / 0.35 (23271) hydrogen bonds : bond 0.04333 / 2.89 ( 946) hydrogen bonds : angle 3.78077 / 2.74 ( 2387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8242 (mt) cc_final: 0.8006 (mt) REVERT: A 63 ILE cc_start: 0.9601 (mm) cc_final: 0.9332 (mm) REVERT: A 68 PHE cc_start: 0.9846 (t80) cc_final: 0.9437 (t80) REVERT: A 74 GLU cc_start: 0.8775 (tt0) cc_final: 0.8198 (tt0) REVERT: A 97 CYS cc_start: 0.9657 (m) cc_final: 0.9379 (p) REVERT: A 118 VAL cc_start: 0.9581 (t) cc_final: 0.9282 (p) REVERT: A 121 MET cc_start: 0.8730 (mmp) cc_final: 0.8135 (mmm) REVERT: B 69 ASP cc_start: 0.9536 (m-30) cc_final: 0.9295 (m-30) REVERT: C 26 PHE cc_start: 0.8559 (m-10) cc_final: 0.7922 (m-80) REVERT: C 39 ASN cc_start: 0.9050 (m110) cc_final: 0.8795 (t0) REVERT: C 90 ASN cc_start: 0.9341 (m110) cc_final: 0.9124 (m110) REVERT: D 77 GLU cc_start: 0.9443 (tp30) cc_final: 0.9179 (tp30) REVERT: D 85 ASN cc_start: 0.8994 (m110) cc_final: 0.8670 (p0) REVERT: D 87 ARG cc_start: 0.9512 (mmt-90) cc_final: 0.9196 (mmm160) REVERT: D 90 ILE cc_start: 0.8780 (mm) cc_final: 0.8425 (mm) REVERT: D 95 ILE cc_start: 0.9863 (tt) cc_final: 0.9610 (pt) REVERT: D 96 GLN cc_start: 0.9334 (tm130) cc_final: 0.9127 (tm-30) REVERT: D 100 ARG cc_start: 0.9198 (mtp180) cc_final: 0.8854 (mmm-85) REVERT: D 102 LEU cc_start: 0.9398 (mm) cc_final: 0.8850 (mm) REVERT: D 103 LEU cc_start: 0.9411 (mt) cc_final: 0.9063 (tp) REVERT: D 106 GLU cc_start: 0.9215 (pm20) cc_final: 0.8877 (pm20) REVERT: D 107 LEU cc_start: 0.9738 (mm) cc_final: 0.9532 (mm) REVERT: E 106 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9205 (tm-30) REVERT: E 111 CYS cc_start: 0.9317 (t) cc_final: 0.9008 (t) REVERT: E 121 MET cc_start: 0.8754 (tpp) cc_final: 0.8276 (tpt) REVERT: F 38 LEU cc_start: 0.9732 (mm) cc_final: 0.9484 (mm) REVERT: F 45 LYS cc_start: 0.8881 (ptpt) cc_final: 0.8619 (ptpt) REVERT: F 54 GLU cc_start: 0.9499 (tp30) cc_final: 0.9097 (tt0) REVERT: F 59 LEU cc_start: 0.9670 (mm) cc_final: 0.9459 (mm) REVERT: F 69 ASP cc_start: 0.9605 (m-30) cc_final: 0.9329 (m-30) REVERT: F 86 ASP cc_start: 0.9009 (m-30) cc_final: 0.8748 (t0) REVERT: F 97 THR cc_start: 0.9345 (m) cc_final: 0.8981 (p) REVERT: G 39 ASN cc_start: 0.9117 (m110) cc_final: 0.8439 (m-40) REVERT: G 64 LEU cc_start: 0.9821 (mt) cc_final: 0.9545 (pp) REVERT: G 65 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9244 (tm-30) REVERT: G 91 ASP cc_start: 0.9234 (t70) cc_final: 0.8507 (t70) REVERT: G 93 GLU cc_start: 0.9667 (mp0) cc_final: 0.9364 (pm20) REVERT: G 105 GLN cc_start: 0.9375 (mp10) cc_final: 0.8768 (mp10) REVERT: H 68 ASN cc_start: 0.9458 (m110) cc_final: 0.8856 (t0) REVERT: H 95 ILE cc_start: 0.9749 (mt) cc_final: 0.9515 (tt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.0961 time to fit residues: 36.9210 Evaluate side-chains 192 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 168 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 139 optimal weight: 50.0000 chunk 70 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN B 94 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.087321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053380 restraints weight = 83368.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054452 restraints weight = 48023.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.055257 restraints weight = 33263.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055742 restraints weight = 25816.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056122 restraints weight = 21643.573| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 16249 Z= 0.147 Angle : 0.632 14.177 23271 Z= 0.357 Chirality : 0.042 0.302 2738 Planarity : 0.004 0.059 2159 Dihedral : 27.114 80.059 4491 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.42 % 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: 1.52 (0.21), residues: 1535 helix: 1.65 (0.21), residues: 605 sheet: 0.83 (0.29), residues: 340 loop : 0.62 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 18 TYR 0.043 0.002 TYR F 89 PHE 0.009 0.001 PHE G 26 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (16249) covalent geometry : angle 0.63188 / 0.36 (23271) hydrogen bonds : bond 0.04573 / 3.09 ( 946) hydrogen bonds : angle 3.85917 / 2.79 ( 2387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.476 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: A 61 LEU cc_start: 0.8257 (mt) cc_final: 0.8033 (mt) REVERT: A 68 PHE cc_start: 0.9842 (t80) cc_final: 0.9590 (t80) REVERT: A 74 GLU cc_start: 0.8791 (tt0) cc_final: 0.8202 (mt-10) REVERT: A 83 LEU cc_start: 0.9210 (mm) cc_final: 0.8984 (mm) REVERT: A 97 CYS cc_start: 0.9367 (m) cc_final: 0.9138 (m) REVERT: A 98 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8941 (mt-10) REVERT: A 106 GLU cc_start: 0.9699 (tt0) cc_final: 0.9386 (tm-30) REVERT: A 121 MET cc_start: 0.8763 (mmp) cc_final: 0.8197 (mmm) REVERT: B 101 PHE cc_start: 0.8812 (m-80) cc_final: 0.8536 (m-10) REVERT: C 26 PHE cc_start: 0.8545 (m-10) cc_final: 0.7895 (m-80) REVERT: C 39 ASN cc_start: 0.9031 (m110) cc_final: 0.8807 (t0) REVERT: C 90 ASN cc_start: 0.9294 (m110) cc_final: 0.9051 (p0) REVERT: D 85 ASN cc_start: 0.8997 (m110) cc_final: 0.8709 (p0) REVERT: D 96 GLN cc_start: 0.9319 (tm-30) cc_final: 0.8760 (tm-30) REVERT: D 100 ARG cc_start: 0.9161 (mtp180) cc_final: 0.8577 (mtp85) REVERT: D 101 LEU cc_start: 0.9425 (tt) cc_final: 0.9187 (tp) REVERT: D 102 LEU cc_start: 0.9384 (mm) cc_final: 0.8984 (mm) REVERT: D 103 LEU cc_start: 0.9404 (mt) cc_final: 0.9114 (tp) REVERT: D 106 GLU cc_start: 0.9176 (pm20) cc_final: 0.8809 (pm20) REVERT: D 107 LEU cc_start: 0.9718 (mm) cc_final: 0.9487 (mm) REVERT: E 106 GLU cc_start: 0.9499 (mt-10) cc_final: 0.9257 (tm-30) REVERT: E 121 MET cc_start: 0.8850 (tpp) cc_final: 0.8321 (tpt) REVERT: F 45 LYS cc_start: 0.8909 (ptpt) cc_final: 0.8624 (ptpt) REVERT: F 54 GLU cc_start: 0.9467 (tp30) cc_final: 0.9086 (tt0) REVERT: F 59 LEU cc_start: 0.9695 (mm) cc_final: 0.9483 (mm) REVERT: F 69 ASP cc_start: 0.9579 (m-30) cc_final: 0.9365 (m-30) REVERT: F 85 MET cc_start: 0.9429 (tpt) cc_final: 0.9125 (tpp) REVERT: F 97 THR cc_start: 0.9393 (m) cc_final: 0.9032 (p) REVERT: G 26 PHE cc_start: 0.9146 (m-10) cc_final: 0.8713 (m-10) REVERT: G 39 ASN cc_start: 0.9104 (m110) cc_final: 0.8422 (m-40) REVERT: G 64 LEU cc_start: 0.9819 (mt) cc_final: 0.9552 (pp) REVERT: G 65 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9227 (tm-30) REVERT: G 91 ASP cc_start: 0.9209 (t70) cc_final: 0.8405 (t70) REVERT: G 93 GLU cc_start: 0.9649 (mp0) cc_final: 0.9301 (pm20) REVERT: G 94 LEU cc_start: 0.9821 (mt) cc_final: 0.9563 (mt) REVERT: G 105 GLN cc_start: 0.9404 (mp10) cc_final: 0.8800 (mp10) REVERT: H 68 ASN cc_start: 0.9473 (m110) cc_final: 0.8862 (t0) REVERT: H 95 ILE cc_start: 0.9760 (mt) cc_final: 0.9528 (tt) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.0989 time to fit residues: 36.2621 Evaluate side-chains 194 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 49 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 159 optimal weight: 50.0000 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 167 optimal weight: 40.0000 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 0.0040 chunk 101 optimal weight: 0.9980 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.3913 r_free = 0.3913 target = 0.089428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.054741 restraints weight = 81454.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055702 restraints weight = 50141.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056360 restraints weight = 36404.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056713 restraints weight = 29064.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.057126 restraints weight = 25292.863| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16249 Z= 0.164 Angle : 0.639 13.485 23271 Z= 0.366 Chirality : 0.042 0.264 2738 Planarity : 0.004 0.068 2159 Dihedral : 27.045 79.959 4491 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.50 (0.21), residues: 1535 helix: 1.51 (0.21), residues: 618 sheet: 0.83 (0.28), residues: 340 loop : 0.73 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.036 0.002 TYR B 52 PHE 0.024 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (16249) covalent geometry : angle 0.63911 / 0.37 (23271) hydrogen bonds : bond 0.05150 / 3.49 ( 946) hydrogen bonds : angle 3.97528 / 2.88 ( 2387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.75 seconds wall clock time: 52 minutes 59.33 seconds (3179.33 seconds total)