Starting phenix.real_space_refine on Fri Jul 3 17:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2p_53536/07_2026/9r2p_53536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2p_53536/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9r2p_53536/07_2026/9r2p_53536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2p_53536/07_2026/9r2p_53536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r2p_53536/07_2026/9r2p_53536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2p_53536/07_2026/9r2p_53536.map" } 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-dev-6108/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: 3.27, per 1000 atoms: 0.21 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: 1.09 Conformation dependent library (CDL) restraints added in 571.9 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: 2.06 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: 3.13 Time building geometry restraints manager: 1.44 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: 20980 1.61 - 3.22: 1820 3.22 - 4.84: 404 4.84 - 6.45: 56 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=" O3' DC J 78 " pdb=" P DG J 79 " pdb=" O5' DG J 79 " ideal model delta sigma weight residual 104.00 96.58 7.42 1.50e+00 4.44e-01 2.45e+01 angle pdb=" O3' DC I 79 " pdb=" P DC I 80 " pdb=" O5' DC I 80 " ideal model delta sigma weight residual 104.00 96.84 7.16 1.50e+00 4.44e-01 2.28e+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: 6.340 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- 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= 0.633 Angle : 0.998 8.061 23271 Z= 0.674 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 0.99805 / 0.67 (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 : 0.302 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: 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: 0.9405 (t80) REVERT: A 74 GLU cc_start: 0.8792 (tt0) cc_final: 0.8074 (mt-10) REVERT: A 86 GLN cc_start: 0.9438 (mt0) cc_final: 0.9196 (mt0) 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: 0.9271 (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: 0.8174 (mtp180) 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: 0.9626 (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: 0.8545 (ttmt) REVERT: F 54 GLU cc_start: 0.9486 (tp30) cc_final: 0.8838 (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: 0.9319 (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: 0.9405 (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: 0.9445 (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: 0.1052 time to fit residues: 50.9205 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 : 0.424 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.0070 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 40.0000 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS G 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.088784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055004 restraints weight = 80882.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.056317 restraints weight = 45695.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057193 restraints weight = 31348.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.057709 restraints weight = 24002.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.058028 restraints weight = 19950.497| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 16249 Z= 0.228 Angle : 0.763 8.764 23271 Z= 0.416 Chirality : 0.046 0.170 2738 Planarity : 0.005 0.041 2159 Dihedral : 28.253 70.370 4491 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.58 % Allowed : 2.60 % Favored : 96.82 % 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: 1.14 (0.21), residues: 1535 helix: 1.20 (0.20), residues: 619 sheet: 0.79 (0.29), residues: 324 loop : 0.45 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 56 TYR 0.023 0.002 TYR D 84 PHE 0.019 0.003 PHE C 26 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.23 (16249) covalent geometry : angle 0.76271 / 0.42 (23271) hydrogen bonds : bond 0.07692 / 5.14 ( 946) hydrogen bonds : angle 4.43995 / 3.26 ( 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 260 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 256 time to evaluate : 0.327 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: A 68 PHE cc_start: 0.9744 (t80) cc_final: 0.9465 (t80) REVERT: A 74 GLU cc_start: 0.8716 (tt0) cc_final: 0.7967 (tt0) REVERT: A 75 ILE cc_start: 0.9781 (mt) cc_final: 0.9514 (mt) REVERT: A 86 GLN cc_start: 0.9565 (mt0) cc_final: 0.9201 (mt0) REVERT: A 94 GLN cc_start: 0.9249 (tt0) cc_final: 0.8510 (tt0) REVERT: A 95 GLU cc_start: 0.9548 (tp30) cc_final: 0.9329 (tp30) REVERT: A 98 GLU cc_start: 0.9431 (mt-10) cc_final: 0.8820 (mt-10) REVERT: A 120 ILE cc_start: 0.9790 (pt) cc_final: 0.9518 (pt) REVERT: B 24 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8197 (mpt180) REVERT: B 63 LEU cc_start: 0.9620 (tp) cc_final: 0.9418 (tt) REVERT: B 69 ASP cc_start: 0.9614 (m-30) cc_final: 0.9407 (m-30) REVERT: B 82 VAL cc_start: 0.9458 (t) cc_final: 0.9234 (t) REVERT: B 86 ASP cc_start: 0.9153 (m-30) cc_final: 0.8684 (t0) REVERT: C 39 ASN cc_start: 0.8547 (m-40) cc_final: 0.8235 (t0) REVERT: D 100 ARG cc_start: 0.9489 (mtp180) cc_final: 0.9082 (mtp180) REVERT: D 102 LEU cc_start: 0.8930 (mt) cc_final: 0.8707 (mt) REVERT: E 56 GLN cc_start: 0.9352 (mt0) cc_final: 0.8956 (pt0) REVERT: E 69 GLN cc_start: 0.9716 (mm-40) cc_final: 0.9469 (mm110) REVERT: E 91 MET cc_start: 0.9527 (mmp) cc_final: 0.8980 (mmm) REVERT: E 106 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9240 (tm-30) REVERT: E 110 LEU cc_start: 0.9661 (mt) cc_final: 0.9401 (mm) REVERT: E 121 MET cc_start: 0.8409 (ttm) cc_final: 0.8056 (ttm) REVERT: F 38 LEU cc_start: 0.9819 (mm) cc_final: 0.9586 (mm) REVERT: F 54 GLU cc_start: 0.9531 (tp30) cc_final: 0.8938 (tt0) REVERT: F 85 MET cc_start: 0.9305 (mmm) cc_final: 0.8837 (mmm) REVERT: F 86 ASP cc_start: 0.8671 (m-30) cc_final: 0.8076 (t70) REVERT: F 97 THR cc_start: 0.9433 (m) cc_final: 0.9229 (t) REVERT: G 26 PHE cc_start: 0.8979 (m-10) cc_final: 0.8206 (m-10) REVERT: G 42 GLU cc_start: 0.9385 (tp30) cc_final: 0.9149 (tp30) REVERT: G 73 ASP cc_start: 0.9225 (m-30) cc_final: 0.9011 (m-30) REVERT: G 91 ASP cc_start: 0.9189 (t70) cc_final: 0.8828 (t70) REVERT: G 93 GLU cc_start: 0.9714 (mp0) cc_final: 0.9359 (tt0) REVERT: G 95 ASN cc_start: 0.9613 (t0) cc_final: 0.9349 (m-40) REVERT: G 97 LEU cc_start: 0.9547 (mt) cc_final: 0.9290 (mt) REVERT: G 105 GLN cc_start: 0.9392 (mp10) cc_final: 0.8819 (mp10) REVERT: H 38 TYR cc_start: 0.9231 (m-80) cc_final: 0.8945 (m-80) REVERT: H 57 SER cc_start: 0.9527 (m) cc_final: 0.9274 (p) REVERT: H 122 TYR cc_start: 0.9347 (t80) cc_final: 0.9021 (t80) outliers start: 4 outliers final: 2 residues processed: 259 average time/residue: 0.0878 time to fit residues: 35.9522 Evaluate side-chains 217 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 50.0000 chunk 21 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 105 optimal weight: 0.2980 chunk 138 optimal weight: 0.0870 chunk 127 optimal weight: 0.4980 chunk 94 optimal weight: 20.0000 chunk 151 optimal weight: 0.0270 chunk 71 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 150 optimal weight: 7.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS B 28 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** 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 = 0.4206 r_free = 0.4206 target = 0.117030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.083021 restraints weight = 144821.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.083509 restraints weight = 66522.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.084807 restraints weight = 43672.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.085290 restraints weight = 30359.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.085512 restraints weight = 24488.293| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2716 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= 0.144 Angle : 0.608 7.879 23271 Z= 0.341 Chirality : 0.043 0.187 2738 Planarity : 0.004 0.039 2159 Dihedral : 27.454 75.476 4491 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.43 % Allowed : 1.45 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.21), residues: 1535 helix: 1.66 (0.20), residues: 616 sheet: 0.89 (0.29), residues: 324 loop : 0.50 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.017 0.002 TYR H 41 PHE 0.020 0.002 PHE E 79 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (16249) covalent geometry : angle 0.60765 / 0.34 (23271) hydrogen bonds : bond 0.05054 / 3.35 ( 946) hydrogen bonds : angle 3.79011 / 2.78 ( 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 281 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 0.471 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: A 68 PHE cc_start: 0.9624 (t80) cc_final: 0.9304 (t80) REVERT: A 94 GLN cc_start: 0.9364 (tt0) cc_final: 0.8601 (tt0) REVERT: A 97 CYS cc_start: 0.9586 (m) cc_final: 0.8969 (m) REVERT: A 98 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8319 (mt-10) REVERT: B 60 LYS cc_start: 0.9722 (ttmm) cc_final: 0.9517 (ptmt) REVERT: B 69 ASP cc_start: 0.9482 (m-30) cc_final: 0.9229 (m-30) REVERT: B 75 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.9094 (mp0) REVERT: B 86 ASP cc_start: 0.9142 (m-30) cc_final: 0.8853 (m-30) REVERT: C 26 PHE cc_start: 0.8513 (m-10) cc_final: 0.8240 (m-10) REVERT: C 39 ASN cc_start: 0.8540 (m-40) cc_final: 0.8301 (t0) REVERT: C 84 LEU cc_start: 0.9586 (mp) cc_final: 0.9307 (mp) REVERT: C 88 ILE cc_start: 0.9602 (mt) cc_final: 0.9392 (tp) REVERT: C 91 ASP cc_start: 0.9116 (t0) cc_final: 0.8910 (t0) REVERT: D 77 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8934 (mm-30) REVERT: D 85 ASN cc_start: 0.9242 (m110) cc_final: 0.8881 (p0) REVERT: D 100 ARG cc_start: 0.9426 (mtp180) cc_final: 0.8922 (mtp180) REVERT: D 106 GLU cc_start: 0.9378 (tp30) cc_final: 0.9170 (tm-30) REVERT: E 47 VAL cc_start: 0.8816 (t) cc_final: 0.7843 (t) REVERT: E 56 GLN cc_start: 0.9234 (mt0) cc_final: 0.8814 (pt0) REVERT: E 91 MET cc_start: 0.9429 (mmp) cc_final: 0.9197 (mmm) REVERT: E 93 LEU cc_start: 0.9791 (mm) cc_final: 0.9446 (mm) REVERT: E 95 GLU cc_start: 0.9521 (mm-30) cc_final: 0.9035 (mm-30) REVERT: E 98 GLU cc_start: 0.9300 (pp20) cc_final: 0.9084 (pp20) REVERT: E 121 MET cc_start: 0.8350 (ttm) cc_final: 0.8000 (ttm) REVERT: F 38 LEU cc_start: 0.9767 (mm) cc_final: 0.9535 (mm) REVERT: F 54 GLU cc_start: 0.9378 (tp30) cc_final: 0.9026 (tt0) REVERT: F 85 MET cc_start: 0.9159 (mmm) cc_final: 0.8720 (mmm) REVERT: F 86 ASP cc_start: 0.8666 (m-30) cc_final: 0.8199 (t70) REVERT: G 65 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9204 (tm-30) REVERT: G 91 ASP cc_start: 0.9210 (t70) cc_final: 0.8770 (t70) REVERT: G 93 GLU cc_start: 0.9602 (mp0) cc_final: 0.9272 (tt0) REVERT: G 95 ASN cc_start: 0.9581 (t0) cc_final: 0.9354 (m-40) REVERT: G 105 GLN cc_start: 0.9280 (mp10) cc_final: 0.8610 (mp10) REVERT: H 57 SER cc_start: 0.9503 (m) cc_final: 0.9217 (p) REVERT: H 66 PHE cc_start: 0.9613 (t80) cc_final: 0.9368 (t80) REVERT: H 68 ASN cc_start: 0.9522 (m110) cc_final: 0.8967 (t0) REVERT: H 101 LEU cc_start: 0.9432 (tp) cc_final: 0.9063 (tp) REVERT: H 107 LEU cc_start: 0.9469 (mt) cc_final: 0.9077 (mt) REVERT: H 122 TYR cc_start: 0.9211 (t80) cc_final: 0.8902 (t80) outliers start: 3 outliers final: 0 residues processed: 279 average time/residue: 0.1039 time to fit residues: 44.5407 Evaluate side-chains 213 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 9.9990 chunk 100 optimal weight: 0.5980 chunk 84 optimal weight: 50.0000 chunk 105 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 127 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 overall best weight: 1.3140 ------------------------------------------------------------------------------- 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** E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.090467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055746 restraints weight = 81332.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.057066 restraints weight = 44671.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.057825 restraints weight = 29964.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.058478 restraints weight = 23104.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058815 restraints weight = 19219.209| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16249 Z= 0.148 Angle : 0.606 13.863 23271 Z= 0.342 Chirality : 0.041 0.175 2738 Planarity : 0.004 0.055 2159 Dihedral : 27.139 71.804 4491 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 1.57 (0.21), residues: 1535 helix: 1.79 (0.21), residues: 612 sheet: 0.93 (0.29), residues: 324 loop : 0.46 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 79 TYR 0.028 0.002 TYR H 84 PHE 0.016 0.002 PHE B 62 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (16249) covalent geometry : angle 0.60596 / 0.34 (23271) hydrogen bonds : bond 0.05051 / 3.38 ( 946) hydrogen bonds : angle 3.74328 / 2.74 ( 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 252 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.431 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: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9091 (p) cc_final: 0.8879 (p) REVERT: A 61 LEU cc_start: 0.8542 (mt) cc_final: 0.8243 (mt) REVERT: B 61 VAL cc_start: 0.9676 (m) cc_final: 0.9376 (m) REVERT: B 69 ASP cc_start: 0.9516 (m-30) cc_final: 0.9115 (m-30) REVERT: C 26 PHE cc_start: 0.8670 (m-10) cc_final: 0.8196 (m-10) REVERT: C 39 ASN cc_start: 0.8636 (m-40) cc_final: 0.8254 (t0) REVERT: C 84 LEU cc_start: 0.9640 (mp) cc_final: 0.9383 (mp) REVERT: C 88 ILE cc_start: 0.9620 (mt) cc_final: 0.9377 (tp) REVERT: D 85 ASN cc_start: 0.9162 (m110) cc_final: 0.8801 (p0) REVERT: D 96 GLN cc_start: 0.9605 (tm-30) cc_final: 0.9031 (tm-30) REVERT: D 100 ARG cc_start: 0.9426 (mtp180) cc_final: 0.8827 (mmm-85) REVERT: E 56 GLN cc_start: 0.9408 (mt0) cc_final: 0.8909 (pt0) REVERT: E 95 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9074 (mm-30) REVERT: E 121 MET cc_start: 0.8191 (ttm) cc_final: 0.7841 (ttm) REVERT: F 38 LEU cc_start: 0.9780 (mm) cc_final: 0.9523 (mm) REVERT: F 54 GLU cc_start: 0.9469 (tp30) cc_final: 0.9046 (tt0) REVERT: F 69 ASP cc_start: 0.9561 (m-30) cc_final: 0.9338 (m-30) REVERT: F 75 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9008 (tm-30) REVERT: F 85 MET cc_start: 0.9388 (mmm) cc_final: 0.8926 (mmm) REVERT: F 86 ASP cc_start: 0.8831 (m-30) cc_final: 0.8335 (t70) REVERT: G 26 PHE cc_start: 0.8975 (m-10) cc_final: 0.8135 (m-10) REVERT: G 91 ASP cc_start: 0.9195 (t70) cc_final: 0.8617 (t70) REVERT: G 93 GLU cc_start: 0.9702 (mp0) cc_final: 0.9324 (mp0) REVERT: G 95 ASN cc_start: 0.9589 (t0) cc_final: 0.9317 (m-40) REVERT: G 97 LEU cc_start: 0.9503 (mt) cc_final: 0.9254 (mt) REVERT: G 105 GLN cc_start: 0.9335 (mp10) cc_final: 0.8682 (mp10) REVERT: H 57 SER cc_start: 0.9441 (m) cc_final: 0.9149 (p) REVERT: H 68 ASN cc_start: 0.9476 (m110) cc_final: 0.8965 (t0) REVERT: H 69 ASP cc_start: 0.9574 (t70) cc_final: 0.9369 (t0) REVERT: H 122 TYR cc_start: 0.9382 (t80) cc_final: 0.9165 (t80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.0933 time to fit residues: 37.0317 Evaluate side-chains 214 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 30.0000 chunk 154 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 129 optimal weight: 50.0000 chunk 134 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.088390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.054051 restraints weight = 82425.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.055313 restraints weight = 46268.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056082 restraints weight = 31597.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.056643 restraints weight = 24576.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057014 restraints weight = 20541.571| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3529 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= 0.180 Angle : 0.602 12.005 23271 Z= 0.347 Chirality : 0.041 0.306 2738 Planarity : 0.004 0.035 2159 Dihedral : 27.060 74.056 4491 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 1.58 (0.21), residues: 1535 helix: 1.73 (0.20), residues: 616 sheet: 0.97 (0.29), residues: 324 loop : 0.51 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 54 TYR 0.013 0.002 TYR E 55 PHE 0.019 0.002 PHE B 101 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (16249) covalent geometry : angle 0.60199 / 0.35 (23271) hydrogen bonds : bond 0.05807 / 3.89 ( 946) hydrogen bonds : angle 3.81163 / 2.79 ( 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 240 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.484 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: A 95 GLU cc_start: 0.9336 (tp30) cc_final: 0.7781 (tp30) REVERT: A 97 CYS cc_start: 0.9525 (m) cc_final: 0.9270 (m) REVERT: A 98 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8787 (pp20) REVERT: B 51 ILE cc_start: 0.9341 (mm) cc_final: 0.9107 (mm) REVERT: B 61 VAL cc_start: 0.9673 (m) cc_final: 0.9108 (m) REVERT: B 65 ASN cc_start: 0.9463 (m-40) cc_final: 0.9111 (m-40) REVERT: B 86 ASP cc_start: 0.9103 (t0) cc_final: 0.8588 (t0) REVERT: C 26 PHE cc_start: 0.8762 (m-10) cc_final: 0.8246 (m-10) REVERT: C 39 ASN cc_start: 0.8722 (m-40) cc_final: 0.8380 (t0) REVERT: C 84 LEU cc_start: 0.9614 (mp) cc_final: 0.9395 (mp) REVERT: C 88 ILE cc_start: 0.9617 (mt) cc_final: 0.9404 (tp) REVERT: C 116 LEU cc_start: 0.8788 (tt) cc_final: 0.8441 (tt) REVERT: D 96 GLN cc_start: 0.9548 (tm-30) cc_final: 0.9276 (tm-30) REVERT: D 100 ARG cc_start: 0.9449 (mtp180) cc_final: 0.9162 (mtp180) REVERT: D 102 LEU cc_start: 0.9346 (mm) cc_final: 0.8927 (mm) REVERT: D 106 GLU cc_start: 0.9567 (tp30) cc_final: 0.9349 (tm-30) REVERT: E 52 ILE cc_start: 0.8877 (mm) cc_final: 0.8636 (mm) REVERT: E 56 GLN cc_start: 0.9449 (mt0) cc_final: 0.8964 (pt0) REVERT: E 95 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9013 (mm-30) REVERT: E 98 GLU cc_start: 0.9275 (pp20) cc_final: 0.8923 (pp20) REVERT: E 125 ILE cc_start: 0.9772 (mt) cc_final: 0.9549 (mt) REVERT: E 127 LEU cc_start: 0.9637 (mm) cc_final: 0.9396 (tt) REVERT: F 38 LEU cc_start: 0.9801 (mm) cc_final: 0.9559 (mm) REVERT: F 54 GLU cc_start: 0.9494 (tp30) cc_final: 0.9058 (tt0) REVERT: F 75 GLU cc_start: 0.9333 (tm-30) cc_final: 0.9005 (tm-30) REVERT: F 85 MET cc_start: 0.9408 (mmm) cc_final: 0.8915 (mmm) REVERT: F 86 ASP cc_start: 0.8917 (m-30) cc_final: 0.8409 (t70) REVERT: G 26 PHE cc_start: 0.9027 (m-10) cc_final: 0.8233 (m-10) REVERT: G 42 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 91 ASP cc_start: 0.9213 (t70) cc_final: 0.8642 (t70) REVERT: G 93 GLU cc_start: 0.9668 (mp0) cc_final: 0.9301 (mp0) REVERT: G 94 LEU cc_start: 0.9671 (mt) cc_final: 0.9457 (mt) REVERT: G 95 ASN cc_start: 0.9571 (t0) cc_final: 0.9338 (m-40) REVERT: G 105 GLN cc_start: 0.9320 (mp10) cc_final: 0.8668 (mp10) REVERT: H 57 SER cc_start: 0.9443 (m) cc_final: 0.9151 (p) REVERT: H 68 ASN cc_start: 0.9488 (m110) cc_final: 0.8948 (t0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0936 time to fit residues: 36.1816 Evaluate side-chains 205 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 170 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4170 r_free = 0.4170 target = 0.114307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.078452 restraints weight = 145218.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080331 restraints weight = 64284.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.080705 restraints weight = 36545.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081674 restraints weight = 27887.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.081593 restraints weight = 23150.809| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16249 Z= 0.149 Angle : 0.581 15.743 23271 Z= 0.332 Chirality : 0.041 0.309 2738 Planarity : 0.004 0.042 2159 Dihedral : 26.987 75.257 4491 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % 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: 1.76 (0.21), residues: 1535 helix: 1.98 (0.20), residues: 610 sheet: 0.81 (0.29), residues: 340 loop : 0.66 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 93 TYR 0.012 0.002 TYR A 55 PHE 0.015 0.002 PHE B 62 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (16249) covalent geometry : angle 0.58113 / 0.33 (23271) hydrogen bonds : bond 0.04483 / 3.01 ( 946) hydrogen bonds : angle 3.62396 / 2.67 ( 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 245 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.458 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: B 51 ILE cc_start: 0.9399 (mm) cc_final: 0.9183 (mm) REVERT: B 61 VAL cc_start: 0.9630 (m) cc_final: 0.9317 (m) REVERT: B 69 ASP cc_start: 0.9470 (m-30) cc_final: 0.8928 (m-30) REVERT: B 86 ASP cc_start: 0.8887 (t0) cc_final: 0.8499 (t0) REVERT: C 39 ASN cc_start: 0.8653 (m-40) cc_final: 0.8376 (m110) REVERT: C 84 LEU cc_start: 0.9683 (mp) cc_final: 0.9434 (mp) REVERT: C 116 LEU cc_start: 0.8856 (tt) cc_final: 0.8391 (mm) REVERT: D 102 LEU cc_start: 0.9378 (mm) cc_final: 0.9112 (mm) REVERT: D 107 LEU cc_start: 0.9739 (mt) cc_final: 0.9155 (mt) REVERT: E 52 ILE cc_start: 0.8837 (mm) cc_final: 0.8433 (mm) REVERT: E 56 GLN cc_start: 0.9342 (mt0) cc_final: 0.8877 (pt0) REVERT: E 95 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8848 (mm-30) REVERT: E 98 GLU cc_start: 0.9201 (pp20) cc_final: 0.8861 (pp20) REVERT: E 121 MET cc_start: 0.8307 (ttm) cc_final: 0.8013 (tpp) REVERT: E 125 ILE cc_start: 0.9774 (mt) cc_final: 0.9516 (mt) REVERT: E 127 LEU cc_start: 0.9635 (mm) cc_final: 0.9417 (tt) REVERT: F 38 LEU cc_start: 0.9777 (mm) cc_final: 0.9562 (mm) REVERT: F 45 LYS cc_start: 0.8678 (ptpt) cc_final: 0.8194 (ptmt) REVERT: F 54 GLU cc_start: 0.9318 (tp30) cc_final: 0.8997 (tt0) REVERT: F 69 ASP cc_start: 0.9375 (m-30) cc_final: 0.9082 (m-30) REVERT: F 75 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8791 (tm-30) REVERT: F 85 MET cc_start: 0.9223 (mmm) cc_final: 0.8794 (mmm) REVERT: F 86 ASP cc_start: 0.8751 (m-30) cc_final: 0.8442 (t70) REVERT: G 26 PHE cc_start: 0.9040 (m-10) cc_final: 0.8331 (m-10) REVERT: G 39 ASN cc_start: 0.9135 (m-40) cc_final: 0.8397 (t0) REVERT: G 91 ASP cc_start: 0.9141 (t70) cc_final: 0.7998 (t70) REVERT: G 93 GLU cc_start: 0.9534 (mp0) cc_final: 0.9227 (pm20) REVERT: G 94 LEU cc_start: 0.9545 (mt) cc_final: 0.9271 (mt) REVERT: G 105 GLN cc_start: 0.9261 (mp10) cc_final: 0.8591 (mp10) REVERT: H 57 SER cc_start: 0.9421 (m) cc_final: 0.9051 (p) REVERT: H 68 ASN cc_start: 0.9516 (m110) cc_final: 0.8891 (t0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.0918 time to fit residues: 36.3683 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 : 0.290 ------------------------------------------------------------------------------- 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: 3.9990 chunk 131 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 4 optimal weight: 0.0980 chunk 151 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 overall best weight: 5.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 = 0.3861 r_free = 0.3861 target = 0.083213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.050761 restraints weight = 85223.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.051736 restraints weight = 51515.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052384 restraints weight = 36693.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052912 restraints weight = 29155.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053238 restraints weight = 24820.704| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 16249 Z= 0.324 Angle : 0.743 10.210 23271 Z= 0.424 Chirality : 0.044 0.265 2738 Planarity : 0.006 0.051 2159 Dihedral : 27.152 76.815 4491 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 1.22 (0.21), residues: 1535 helix: 1.18 (0.20), residues: 615 sheet: 0.87 (0.29), residues: 340 loop : 0.56 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 79 TYR 0.020 0.002 TYR H 38 PHE 0.016 0.002 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.003 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.32 (16249) covalent geometry : angle 0.74341 / 0.42 (23271) hydrogen bonds : bond 0.10316 / 7.02 ( 946) hydrogen bonds : angle 4.33736 / 3.19 ( 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 220 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.441 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 65 LYS cc_start: 0.9749 (mptt) cc_final: 0.9451 (mmtm) REVERT: A 68 PHE cc_start: 0.9761 (t80) cc_final: 0.9459 (t80) REVERT: A 74 GLU cc_start: 0.8730 (tt0) cc_final: 0.8151 (mt-10) REVERT: A 83 LEU cc_start: 0.9439 (tp) cc_final: 0.8998 (mt) REVERT: B 64 GLU cc_start: 0.9640 (pm20) cc_final: 0.9397 (pm20) REVERT: B 65 ASN cc_start: 0.9522 (t0) cc_final: 0.9303 (t0) REVERT: B 69 ASP cc_start: 0.9548 (m-30) cc_final: 0.9253 (m-30) REVERT: B 86 ASP cc_start: 0.9306 (t0) cc_final: 0.9038 (t0) REVERT: C 26 PHE cc_start: 0.8799 (m-10) cc_final: 0.7957 (m-10) REVERT: C 39 ASN cc_start: 0.8970 (m-40) cc_final: 0.8638 (m-40) REVERT: C 116 LEU cc_start: 0.8875 (tt) cc_final: 0.8419 (mm) REVERT: D 100 ARG cc_start: 0.9442 (mtp180) cc_final: 0.9181 (mtp85) REVERT: D 102 LEU cc_start: 0.9465 (mm) cc_final: 0.9252 (mm) REVERT: E 52 ILE cc_start: 0.9159 (mm) cc_final: 0.8924 (mm) REVERT: E 56 GLN cc_start: 0.9542 (mt0) cc_final: 0.9086 (pt0) REVERT: E 91 MET cc_start: 0.9448 (mmp) cc_final: 0.9057 (mmm) REVERT: E 95 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9133 (mm-30) REVERT: E 121 MET cc_start: 0.8471 (ttm) cc_final: 0.7777 (ttm) REVERT: E 125 ILE cc_start: 0.9786 (mt) cc_final: 0.9525 (mt) REVERT: F 45 LYS cc_start: 0.8923 (ptpt) cc_final: 0.8533 (ptmt) REVERT: F 54 GLU cc_start: 0.9562 (tp30) cc_final: 0.9118 (tt0) REVERT: F 59 LEU cc_start: 0.9673 (mt) cc_final: 0.9466 (mt) REVERT: F 69 ASP cc_start: 0.9552 (m-30) cc_final: 0.9270 (m-30) REVERT: F 85 MET cc_start: 0.9377 (mmm) cc_final: 0.9056 (mmp) REVERT: F 86 ASP cc_start: 0.9060 (m-30) cc_final: 0.8533 (t0) REVERT: G 26 PHE cc_start: 0.9180 (m-10) cc_final: 0.8969 (m-10) REVERT: G 39 ASN cc_start: 0.9149 (m-40) cc_final: 0.8508 (t0) REVERT: G 91 ASP cc_start: 0.9186 (t70) cc_final: 0.8585 (t70) REVERT: G 93 GLU cc_start: 0.9683 (mp0) cc_final: 0.9209 (pm20) REVERT: G 95 ASN cc_start: 0.9616 (t0) cc_final: 0.9389 (m-40) REVERT: G 105 GLN cc_start: 0.9345 (mp10) cc_final: 0.8766 (mp10) REVERT: H 57 SER cc_start: 0.9484 (m) cc_final: 0.9097 (p) REVERT: H 68 ASN cc_start: 0.9504 (m110) cc_final: 0.8978 (t0) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0925 time to fit residues: 32.7239 Evaluate side-chains 180 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 104 optimal weight: 40.0000 chunk 48 optimal weight: 1.9990 chunk 172 optimal weight: 50.0000 chunk 155 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3902 r_free = 0.3902 target = 0.085593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.052017 restraints weight = 84590.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052916 restraints weight = 50123.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053609 restraints weight = 34120.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.054199 restraints weight = 26416.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054573 restraints weight = 22106.655| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 16249 Z= 0.196 Angle : 0.629 13.593 23271 Z= 0.364 Chirality : 0.043 0.286 2738 Planarity : 0.005 0.072 2159 Dihedral : 27.324 80.295 4491 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 1.49 (0.21), residues: 1535 helix: 1.51 (0.20), residues: 615 sheet: 0.92 (0.29), residues: 340 loop : 0.63 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG G 18 TYR 0.017 0.002 TYR E 100 PHE 0.022 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.014 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 (16249) covalent geometry : angle 0.62902 / 0.36 (23271) hydrogen bonds : bond 0.06010 / 4.07 ( 946) hydrogen bonds : angle 4.00287 / 2.94 ( 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 225 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.457 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 52 ILE cc_start: 0.9264 (mm) cc_final: 0.9006 (mm) REVERT: A 65 LYS cc_start: 0.9711 (mptt) cc_final: 0.9457 (mmtm) REVERT: A 82 ASP cc_start: 0.9126 (m-30) cc_final: 0.8708 (p0) REVERT: A 83 LEU cc_start: 0.9440 (tp) cc_final: 0.8904 (mt) REVERT: A 94 GLN cc_start: 0.9267 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 97 CYS cc_start: 0.9560 (m) cc_final: 0.9333 (m) REVERT: B 65 ASN cc_start: 0.9527 (t0) cc_final: 0.9326 (t0) REVERT: B 69 ASP cc_start: 0.9477 (m-30) cc_final: 0.9103 (m-30) REVERT: B 91 LEU cc_start: 0.9675 (mt) cc_final: 0.9460 (mt) REVERT: C 26 PHE cc_start: 0.8609 (m-10) cc_final: 0.8044 (m-10) REVERT: C 39 ASN cc_start: 0.8976 (m-40) cc_final: 0.8732 (t0) REVERT: D 60 MET cc_start: 0.8975 (tpt) cc_final: 0.8675 (tpt) REVERT: D 100 ARG cc_start: 0.9357 (mtp180) cc_final: 0.9123 (mtp85) REVERT: E 52 ILE cc_start: 0.9147 (mm) cc_final: 0.8855 (mm) REVERT: E 56 GLN cc_start: 0.9518 (mt0) cc_final: 0.9012 (pt0) REVERT: E 95 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9031 (mm-30) REVERT: E 98 GLU cc_start: 0.9280 (pp20) cc_final: 0.8925 (pp20) REVERT: E 121 MET cc_start: 0.8324 (ttm) cc_final: 0.8116 (tpp) REVERT: E 125 ILE cc_start: 0.9774 (mt) cc_final: 0.9514 (mt) REVERT: F 54 GLU cc_start: 0.9523 (tp30) cc_final: 0.9099 (tt0) REVERT: F 59 LEU cc_start: 0.9634 (mt) cc_final: 0.9417 (mt) REVERT: F 69 ASP cc_start: 0.9549 (m-30) cc_final: 0.9315 (m-30) REVERT: F 75 GLU cc_start: 0.9319 (tm-30) cc_final: 0.8977 (tm-30) REVERT: F 85 MET cc_start: 0.9344 (mmm) cc_final: 0.8987 (mmp) REVERT: F 86 ASP cc_start: 0.8980 (m-30) cc_final: 0.8454 (t0) REVERT: G 26 PHE cc_start: 0.9143 (m-10) cc_final: 0.8915 (m-10) REVERT: G 91 ASP cc_start: 0.9317 (t70) cc_final: 0.8070 (t70) REVERT: G 93 GLU cc_start: 0.9647 (mp0) cc_final: 0.9274 (pm20) REVERT: G 94 LEU cc_start: 0.9782 (mm) cc_final: 0.9416 (mp) REVERT: G 98 LEU cc_start: 0.9525 (mt) cc_final: 0.9245 (pp) REVERT: G 105 GLN cc_start: 0.9316 (mp10) cc_final: 0.8725 (mp10) REVERT: H 57 SER cc_start: 0.9466 (m) cc_final: 0.9092 (p) REVERT: H 68 ASN cc_start: 0.9503 (m110) cc_final: 0.8932 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0936 time to fit residues: 34.3688 Evaluate side-chains 189 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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: 3.9990 chunk 141 optimal weight: 3.9990 chunk 161 optimal weight: 0.0000 chunk 105 optimal weight: 6.9990 chunk 103 optimal weight: 40.0000 chunk 12 optimal weight: 0.8980 chunk 129 optimal weight: 40.0000 chunk 69 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.086535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052990 restraints weight = 82495.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.054136 restraints weight = 47379.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.054963 restraints weight = 32778.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055540 restraints weight = 25086.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055885 restraints weight = 20914.375| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16249 Z= 0.159 Angle : 0.610 12.946 23271 Z= 0.352 Chirality : 0.042 0.283 2738 Planarity : 0.004 0.068 2159 Dihedral : 27.188 80.694 4491 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 1.70 (0.21), residues: 1535 helix: 1.73 (0.21), residues: 616 sheet: 0.97 (0.29), residues: 340 loop : 0.74 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 18 TYR 0.051 0.002 TYR H 84 PHE 0.029 0.002 PHE B 62 TRP 0.000 0.000 TRP K 146 HIS 0.014 0.002 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (16249) covalent geometry : angle 0.60960 / 0.35 (23271) hydrogen bonds : bond 0.05073 / 3.38 ( 946) hydrogen bonds : angle 3.83331 / 2.81 ( 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 229 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.467 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: A 52 ILE cc_start: 0.9257 (mm) cc_final: 0.8817 (mm) REVERT: A 65 LYS cc_start: 0.9663 (mptt) cc_final: 0.9450 (mmtm) REVERT: A 68 PHE cc_start: 0.9715 (t80) cc_final: 0.9347 (t80) REVERT: A 83 LEU cc_start: 0.9399 (tp) cc_final: 0.8962 (mt) REVERT: A 94 GLN cc_start: 0.9230 (tt0) cc_final: 0.8727 (tt0) REVERT: A 97 CYS cc_start: 0.9544 (m) cc_final: 0.9336 (m) REVERT: B 41 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8558 (mmm160) REVERT: C 26 PHE cc_start: 0.8569 (m-10) cc_final: 0.7954 (m-10) REVERT: C 39 ASN cc_start: 0.8928 (m-40) cc_final: 0.8574 (m-40) REVERT: C 42 GLU cc_start: 0.9085 (tp30) cc_final: 0.8780 (tp30) REVERT: C 90 ASN cc_start: 0.9287 (m110) cc_final: 0.9074 (m110) REVERT: D 77 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9230 (tp30) REVERT: D 102 LEU cc_start: 0.9336 (mm) cc_final: 0.8996 (mm) REVERT: E 56 GLN cc_start: 0.9507 (mt0) cc_final: 0.8969 (pt0) REVERT: E 95 GLU cc_start: 0.9411 (mm-30) cc_final: 0.8999 (mm-30) REVERT: E 98 GLU cc_start: 0.9247 (pp20) cc_final: 0.8873 (pp20) REVERT: E 125 ILE cc_start: 0.9780 (mt) cc_final: 0.9509 (mt) REVERT: F 38 LEU cc_start: 0.9828 (mm) cc_final: 0.9598 (pp) REVERT: F 54 GLU cc_start: 0.9527 (tp30) cc_final: 0.9110 (tt0) REVERT: F 69 ASP cc_start: 0.9533 (m-30) cc_final: 0.9295 (m-30) REVERT: F 75 GLU cc_start: 0.9320 (tm-30) cc_final: 0.8978 (tm-30) REVERT: F 85 MET cc_start: 0.9312 (mmm) cc_final: 0.8927 (mmp) REVERT: F 86 ASP cc_start: 0.8928 (m-30) cc_final: 0.8438 (t0) REVERT: G 39 ASN cc_start: 0.9186 (m-40) cc_final: 0.8548 (t0) REVERT: G 91 ASP cc_start: 0.9330 (t70) cc_final: 0.8371 (t70) REVERT: G 93 GLU cc_start: 0.9633 (mp0) cc_final: 0.9267 (pm20) REVERT: G 94 LEU cc_start: 0.9772 (mm) cc_final: 0.9513 (mt) REVERT: G 98 LEU cc_start: 0.9450 (mt) cc_final: 0.9178 (pp) REVERT: G 105 GLN cc_start: 0.9289 (mp10) cc_final: 0.8658 (mp10) REVERT: H 57 SER cc_start: 0.9429 (m) cc_final: 0.9213 (p) REVERT: H 68 ASN cc_start: 0.9519 (m110) cc_final: 0.8924 (t0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0971 time to fit residues: 35.9259 Evaluate side-chains 195 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 20.0000 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 168 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 139 optimal weight: 0.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** 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 = 0.3944 r_free = 0.3944 target = 0.088355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.053795 restraints weight = 84192.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054906 restraints weight = 46970.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055740 restraints weight = 32127.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.056204 restraints weight = 24816.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056645 restraints weight = 21114.078| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16249 Z= 0.135 Angle : 0.608 13.757 23271 Z= 0.344 Chirality : 0.042 0.286 2738 Planarity : 0.004 0.059 2159 Dihedral : 27.028 79.248 4491 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 1.84 (0.21), residues: 1535 helix: 1.94 (0.21), residues: 616 sheet: 0.98 (0.29), residues: 340 loop : 0.74 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 93 TYR 0.022 0.002 TYR C 51 PHE 0.010 0.001 PHE E 79 TRP 0.000 0.000 TRP K 146 HIS 0.011 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (16249) covalent geometry : angle 0.60753 / 0.34 (23271) hydrogen bonds : bond 0.04112 / 2.76 ( 946) hydrogen bonds : angle 3.70300 / 2.73 ( 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 230 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.444 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 52 ILE cc_start: 0.9273 (mm) cc_final: 0.8825 (mm) REVERT: A 65 LYS cc_start: 0.9665 (mptt) cc_final: 0.9398 (mmtm) REVERT: A 74 GLU cc_start: 0.8869 (tt0) cc_final: 0.8321 (mt-10) REVERT: A 95 GLU cc_start: 0.9370 (tp30) cc_final: 0.8457 (tp30) REVERT: A 97 CYS cc_start: 0.9533 (m) cc_final: 0.9287 (m) REVERT: A 98 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8693 (pp20) REVERT: B 41 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8517 (mmm160) REVERT: B 65 ASN cc_start: 0.9534 (t0) cc_final: 0.9332 (t0) REVERT: B 69 ASP cc_start: 0.9572 (m-30) cc_final: 0.9221 (m-30) REVERT: B 86 ASP cc_start: 0.9333 (t0) cc_final: 0.9120 (t0) REVERT: C 26 PHE cc_start: 0.8575 (m-10) cc_final: 0.7944 (m-10) REVERT: C 39 ASN cc_start: 0.8983 (m-40) cc_final: 0.8760 (t0) REVERT: C 90 ASN cc_start: 0.9284 (m110) cc_final: 0.9061 (p0) REVERT: D 85 ASN cc_start: 0.8745 (m110) cc_final: 0.8397 (m110) REVERT: D 100 ARG cc_start: 0.9325 (mtp180) cc_final: 0.9001 (mtp85) REVERT: E 95 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9085 (mm-30) REVERT: E 98 GLU cc_start: 0.9227 (pp20) cc_final: 0.8953 (pp20) REVERT: E 111 CYS cc_start: 0.9052 (t) cc_final: 0.8523 (t) REVERT: E 121 MET cc_start: 0.8870 (tpt) cc_final: 0.8527 (tpp) REVERT: E 125 ILE cc_start: 0.9761 (mt) cc_final: 0.9457 (mt) REVERT: F 38 LEU cc_start: 0.9812 (mm) cc_final: 0.9590 (pp) REVERT: F 54 GLU cc_start: 0.9478 (tp30) cc_final: 0.9058 (tt0) REVERT: F 69 ASP cc_start: 0.9514 (m-30) cc_final: 0.9297 (m-30) REVERT: F 75 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8935 (tm-30) REVERT: F 85 MET cc_start: 0.9345 (mmm) cc_final: 0.8879 (mmm) REVERT: F 86 ASP cc_start: 0.8919 (m-30) cc_final: 0.8418 (t0) REVERT: G 26 PHE cc_start: 0.9238 (m-10) cc_final: 0.8816 (m-10) REVERT: G 91 ASP cc_start: 0.9329 (t70) cc_final: 0.8413 (t70) REVERT: G 93 GLU cc_start: 0.9620 (mp0) cc_final: 0.9254 (pm20) REVERT: G 94 LEU cc_start: 0.9764 (mm) cc_final: 0.9494 (mt) REVERT: G 98 LEU cc_start: 0.9421 (mt) cc_final: 0.9155 (pp) REVERT: G 105 GLN cc_start: 0.9229 (mp10) cc_final: 0.8502 (mp10) REVERT: H 57 SER cc_start: 0.9393 (m) cc_final: 0.9172 (p) REVERT: H 68 ASN cc_start: 0.9508 (m110) cc_final: 0.8908 (t0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.0956 time to fit residues: 35.3512 Evaluate side-chains 196 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 1.9990 chunk 159 optimal weight: 50.0000 chunk 177 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 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 = 0.3942 r_free = 0.3942 target = 0.091018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056039 restraints weight = 81159.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057032 restraints weight = 49539.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.057409 restraints weight = 35923.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.058041 restraints weight = 29919.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.058445 restraints weight = 24914.758| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16249 Z= 0.140 Angle : 0.607 13.450 23271 Z= 0.349 Chirality : 0.042 0.245 2738 Planarity : 0.004 0.050 2159 Dihedral : 26.942 78.433 4491 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % 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: 1.81 (0.21), residues: 1535 helix: 1.89 (0.21), residues: 612 sheet: 0.99 (0.29), residues: 340 loop : 0.74 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 18 TYR 0.024 0.002 TYR B 52 PHE 0.049 0.002 PHE A 68 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 0.00260 / 0.14 (16249) covalent geometry : angle 0.60678 / 0.35 (23271) hydrogen bonds : bond 0.04398 / 2.97 ( 946) hydrogen bonds : angle 3.76953 / 2.77 ( 2387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.00 seconds wall clock time: 56 minutes 38.28 seconds (3398.28 seconds total)