Starting phenix.real_space_refine on Thu Jul 2 23:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.cif Found real_map, /net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.map" model { file = "/net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6put_20481/07_2026/6put_20481.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 sd= 0.707 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 66 5.49 5 S 32 5.16 5 C 6610 2.51 5 N 1886 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 10976 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1905 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Chain: "B" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1818 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 4 Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 526 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "F" Number of atoms: 331 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 362 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 317 SG CYS A 40 25.667 45.428 50.550 1.00 37.03 S ATOM 340 SG CYS A 43 29.185 46.359 49.087 1.00 16.24 S ATOM 2224 SG CYS B 40 49.443 121.657 21.753 1.00103.27 S Restraints were copied for chains: G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.50 ... (19 atoms not shown) pdb=" C4 A DA F 21 " occ=0.50 residue: pdb=" P A DA K 21 " occ=0.50 ... (19 atoms not shown) pdb=" C4 A DA K 21 " occ=0.50 Time building chain proxies: 2.19, per 1000 atoms: 0.20 Number of scatterers: 10976 At special positions: 0 Unit cell: (90.85, 133.51, 82.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 32 16.00 P 66 15.00 O 2374 8.00 N 1886 7.00 C 6610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 288.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 16 " Number of angles added : 2 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 47.0% alpha, 18.5% beta 28 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 WARNING: missing atoms! removed outlier: 4.017A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.678A pdb=" N CYS A 43 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 44' Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.507A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.629A pdb=" N VAL A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.520A pdb=" N PHE B 26 " --> pdb=" O MET B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.701A pdb=" N CYS B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 151 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 172 through 186 removed outlier: 3.828A pdb=" N GLN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 removed outlier: 3.627A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'G' and resid 3 through 16 WARNING: missing atoms! removed outlier: 4.017A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 40 through 44 removed outlier: 3.678A pdb=" N CYS G 43 " --> pdb=" O CYS G 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN G 44 " --> pdb=" O ASP G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 44' Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 148 through 165 Processing helix chain 'G' and resid 166 through 169 removed outlier: 3.507A pdb=" N ALA G 169 " --> pdb=" O ARG G 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 166 through 169' Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 195 through 219 removed outlier: 3.629A pdb=" N VAL G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 18 through 26 removed outlier: 3.520A pdb=" N PHE H 26 " --> pdb=" O MET H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.701A pdb=" N CYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 151 through 166 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 172 through 186 removed outlier: 3.828A pdb=" N GLN H 177 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET H 178 " --> pdb=" O THR H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 221 removed outlier: 3.627A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 Processing sheet with id=1, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.069A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=3, first strand: chain 'A' and resid 241 through 244 Processing sheet with id=4, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.319A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.207A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 256 through 261 removed outlier: 6.463A pdb=" N GLN C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU C 241 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY C 237 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR C 227 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 257 through 261 removed outlier: 6.578A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'G' and resid 60 through 61 removed outlier: 6.069A pdb=" N VAL G 113 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'G' and resid 64 through 68 Processing sheet with id=10, first strand: chain 'G' and resid 241 through 244 Processing sheet with id=11, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.319A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 240 through 244 removed outlier: 6.207A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.463A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY I 237 " --> pdb=" O TYR I 227 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR I 227 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 257 through 261 removed outlier: 6.578A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 0.91 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: 2336 1.33 - 1.45: 2572 1.45 - 1.57: 5926 1.57 - 1.69: 130 1.69 - 1.81: 46 Bond restraints: 11010 Sorted by residual: bond pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 1.335 1.480 -0.145 1.38e-02 5.25e+03 1.10e+02 bond pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 1.335 1.480 -0.145 1.38e-02 5.25e+03 1.10e+02 bond pdb=" C3'A DA K 21 " pdb=" C2'A DA K 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3'A DA F 21 " pdb=" C2'A DA F 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC E 19 " pdb=" O3' DC E 19 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.18e+01 ... (remaining 11005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 14898 2.53 - 5.07: 214 5.07 - 7.60: 14 7.60 - 10.13: 0 10.13 - 12.66: 12 Bond angle restraints: 15138 Sorted by residual: angle pdb=" O LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 122.15 109.65 12.50 1.14e+00 7.69e-01 1.20e+02 angle pdb=" O LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 122.15 109.65 12.50 1.14e+00 7.69e-01 1.20e+02 angle pdb=" CA LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 117.39 129.82 -12.43 1.24e+00 6.50e-01 1.01e+02 angle pdb=" CA LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 117.39 129.82 -12.43 1.24e+00 6.50e-01 1.01e+02 angle pdb=" O ASP G 116 " pdb=" C ASP G 116 " pdb=" N ASN G 117 " ideal model delta sigma weight residual 121.83 133.32 -11.49 1.28e+00 6.10e-01 8.05e+01 ... (remaining 15133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5436 17.65 - 35.30: 588 35.30 - 52.95: 300 52.95 - 70.61: 76 70.61 - 88.26: 16 Dihedral angle restraints: 6416 sinusoidal: 3066 harmonic: 3350 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR C 271 " pdb=" C TYR C 271 " pdb=" N GLY C 272 " pdb=" CA GLY C 272 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 6413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1210 0.055 - 0.110: 388 0.110 - 0.164: 76 0.164 - 0.219: 8 0.219 - 0.274: 2 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CB VAL B 165 " pdb=" CA VAL B 165 " pdb=" CG1 VAL B 165 " pdb=" CG2 VAL B 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL H 165 " pdb=" CA VAL H 165 " pdb=" CG1 VAL H 165 " pdb=" CG2 VAL H 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN B 117 " pdb=" N ASN B 117 " pdb=" C ASN B 117 " pdb=" CB ASN B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1681 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 57 " -0.041 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO B 58 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 57 " 0.041 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO H 58 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 58 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 58 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 116 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ASP H 116 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP H 116 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN H 117 " 0.012 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 2 1.96 - 2.94: 4320 2.94 - 3.92: 29776 3.92 - 4.90: 59558 Warning: very small nonbonded interaction distances. Nonbonded interactions: 93666 Sorted by model distance: nonbonded pdb=" O HOH A 438 " pdb=" O HOH K 110 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 459 " pdb=" O HOH G 469 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 469 " pdb=" O HOH G 459 " model vdw 0.000 3.040 nonbonded pdb=" O HOH F 110 " pdb=" O HOH G 438 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 477 " pdb=" O HOH G 478 " model vdw 0.001 3.040 ... (remaining 93661 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 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 : 0.012 0.593 11024 Z= 0.563 Angle : 0.863 12.664 15140 Z= 0.611 Chirality : 0.055 0.274 1684 Planarity : 0.007 0.061 1668 Dihedral : 19.073 88.257 4248 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.43 (0.19), residues: 1130 helix: -2.36 (0.16), residues: 494 sheet: -1.30 (0.31), residues: 216 loop : -2.46 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 262 TYR 0.017 0.002 TYR B 83 PHE 0.015 0.002 PHE G 185 TRP 0.011 0.002 TRP A 19 HIS 0.005 0.002 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.46 (11010) covalent geometry : angle 0.86133 / 0.61 (15138) hydrogen bonds : bond 0.10927 / 6.72 ( 560) hydrogen bonds : angle 6.54535 / 4.56 ( 1550) metal coordination : bond 0.27949 / 16.22 ( 14) metal coordination : angle 4.80314 / 2.68 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.301 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7899 (tm-30) REVERT: A 25 ASP cc_start: 0.8305 (m-30) cc_final: 0.7983 (m-30) REVERT: G 10 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7897 (tm-30) REVERT: G 25 ASP cc_start: 0.8305 (m-30) cc_final: 0.7984 (m-30) outliers start: 2 outliers final: 2 residues processed: 240 average time/residue: 0.5779 time to fit residues: 148.8554 Evaluate side-chains 182 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS B 9 GLN B 216 GLN B 221 GLN G 183 HIS H 12 HIS ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103902 restraints weight = 12435.778| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.66 r_work: 0.3002 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 11024 Z= 0.242 Angle : 0.937 24.179 15140 Z= 0.509 Chirality : 0.053 0.344 1684 Planarity : 0.013 0.249 1668 Dihedral : 21.703 151.082 1976 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.62 % Allowed : 4.42 % Favored : 94.96 % Rotamer: Outliers : 3.74 % Allowed : 13.26 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.21), residues: 1130 helix: -1.54 (0.20), residues: 494 sheet: -1.28 (0.32), residues: 216 loop : -2.52 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.003 ARG J 228 TYR 0.280 0.009 TYR G 226 PHE 0.101 0.005 PHE H 26 TRP 0.132 0.008 TRP H 61 HIS 0.046 0.004 HIS H 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (11010) covalent geometry : angle 0.93694 / 0.51 (15138) hydrogen bonds : bond 0.05085 / 3.35 ( 560) hydrogen bonds : angle 5.88944 / 4.15 ( 1550) metal coordination : bond 0.05075 / 1.71 ( 14) metal coordination : angle 2.49220 / 1.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.403 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 25 ASP cc_start: 0.8359 (m-30) cc_final: 0.7825 (m-30) REVERT: A 242 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 66 THR cc_start: 0.8614 (m) cc_final: 0.7914 (p) REVERT: D 236 LYS cc_start: 0.8958 (mttt) cc_final: 0.8744 (mttt) REVERT: G 10 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G 13 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: G 25 ASP cc_start: 0.8119 (m-30) cc_final: 0.7530 (m-30) REVERT: G 93 THR cc_start: 0.8089 (t) cc_final: 0.7710 (p) REVERT: G 95 GLN cc_start: 0.8389 (tt0) cc_final: 0.7934 (mm110) REVERT: G 216 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7255 (tp40) REVERT: H 11 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7526 (tm-30) REVERT: H 13 GLU cc_start: 0.7777 (pt0) cc_final: 0.6867 (pp20) REVERT: H 60 ILE cc_start: 0.8835 (mt) cc_final: 0.8629 (mm) REVERT: H 252 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7691 (tt0) outliers start: 37 outliers final: 4 residues processed: 233 average time/residue: 0.4874 time to fit residues: 123.2626 Evaluate side-chains 178 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain I residue 261 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 GLN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100018 restraints weight = 12530.640| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.68 r_work: 0.2926 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11024 Z= 0.200 Angle : 0.571 6.258 15140 Z= 0.325 Chirality : 0.046 0.159 1684 Planarity : 0.005 0.057 1668 Dihedral : 21.653 173.376 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.04 % Allowed : 14.78 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.56 (0.22), residues: 1130 helix: -0.08 (0.21), residues: 494 sheet: -0.89 (0.33), residues: 216 loop : -2.19 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 166 TYR 0.028 0.002 TYR G 226 PHE 0.011 0.001 PHE A 185 TRP 0.023 0.002 TRP G 19 HIS 0.010 0.001 HIS H 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (11010) covalent geometry : angle 0.57095 / 0.33 (15138) hydrogen bonds : bond 0.03990 / 2.66 ( 560) hydrogen bonds : angle 4.89015 / 3.42 ( 1550) metal coordination : bond 0.00631 / 0.39 ( 14) metal coordination : angle 1.89305 / 1.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.404 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 119 SER cc_start: 0.8984 (t) cc_final: 0.8783 (p) REVERT: A 242 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 66 THR cc_start: 0.8639 (m) cc_final: 0.7974 (p) REVERT: C 262 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7402 (tpt170) REVERT: G 10 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G 25 ASP cc_start: 0.8185 (m-30) cc_final: 0.7649 (m-30) REVERT: G 95 GLN cc_start: 0.8351 (tt0) cc_final: 0.7855 (mm110) REVERT: G 119 SER cc_start: 0.9026 (t) cc_final: 0.8816 (p) REVERT: G 216 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: H 10 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7393 (tp30) REVERT: H 11 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7379 (tm-30) REVERT: H 13 GLU cc_start: 0.7885 (pt0) cc_final: 0.6817 (pp20) REVERT: H 136 LYS cc_start: 0.8090 (tptp) cc_final: 0.7811 (tttm) REVERT: I 262 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7478 (tpt170) outliers start: 30 outliers final: 15 residues processed: 194 average time/residue: 0.4851 time to fit residues: 102.4596 Evaluate side-chains 182 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN B 252 GLN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.100515 restraints weight = 12480.825| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.67 r_work: 0.2934 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11024 Z= 0.159 Angle : 0.530 5.830 15140 Z= 0.301 Chirality : 0.044 0.147 1684 Planarity : 0.004 0.042 1668 Dihedral : 21.668 175.646 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.63 % Allowed : 15.89 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.70 (0.24), residues: 1130 helix: 0.80 (0.22), residues: 494 sheet: -0.51 (0.33), residues: 216 loop : -1.96 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.013 0.001 TYR G 194 PHE 0.015 0.001 PHE H 26 TRP 0.014 0.001 TRP G 19 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11010) covalent geometry : angle 0.52940 / 0.30 (15138) hydrogen bonds : bond 0.03585 / 2.39 ( 560) hydrogen bonds : angle 4.63214 / 3.23 ( 1550) metal coordination : bond 0.00483 / 0.28 ( 14) metal coordination : angle 1.28026 / 0.73 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.405 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 242 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 10 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7365 (tp30) REVERT: B 11 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7628 (tm-30) REVERT: B 66 THR cc_start: 0.8651 (m) cc_final: 0.8021 (p) REVERT: B 170 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 236 LYS cc_start: 0.8692 (mttm) cc_final: 0.8477 (mmtp) REVERT: C 262 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7014 (tpm170) REVERT: G 10 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7705 (tm-30) REVERT: G 25 ASP cc_start: 0.8193 (m-30) cc_final: 0.7645 (m-30) REVERT: G 95 GLN cc_start: 0.8315 (tt0) cc_final: 0.7811 (mm110) REVERT: G 216 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: G 242 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8312 (mp) REVERT: H 10 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7423 (tp30) REVERT: H 11 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7416 (tm-30) REVERT: H 13 GLU cc_start: 0.7802 (pt0) cc_final: 0.6809 (pp20) REVERT: H 66 THR cc_start: 0.8640 (m) cc_final: 0.8017 (p) REVERT: I 236 LYS cc_start: 0.8682 (mttm) cc_final: 0.8454 (mmtp) REVERT: I 262 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7007 (tpm170) REVERT: J 236 LYS cc_start: 0.8985 (mttt) cc_final: 0.8729 (mttm) outliers start: 26 outliers final: 12 residues processed: 192 average time/residue: 0.4625 time to fit residues: 96.8450 Evaluate side-chains 187 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104062 restraints weight = 12290.128| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.82 r_work: 0.2973 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11024 Z= 0.142 Angle : 0.509 5.844 15140 Z= 0.290 Chirality : 0.043 0.141 1684 Planarity : 0.004 0.041 1668 Dihedral : 21.602 176.873 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.53 % Allowed : 16.60 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.26 (0.24), residues: 1130 helix: 1.20 (0.23), residues: 494 sheet: -0.28 (0.33), residues: 216 loop : -1.79 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.011 0.001 TYR A 194 PHE 0.011 0.001 PHE H 26 TRP 0.011 0.001 TRP G 19 HIS 0.004 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (11010) covalent geometry : angle 0.50872 / 0.29 (15138) hydrogen bonds : bond 0.03379 / 2.25 ( 560) hydrogen bonds : angle 4.48465 / 3.12 ( 1550) metal coordination : bond 0.00424 / 0.25 ( 14) metal coordination : angle 0.86450 / 0.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.380 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 10 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7397 (tp30) REVERT: B 11 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 66 THR cc_start: 0.8715 (m) cc_final: 0.8125 (p) REVERT: C 262 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7389 (tpt170) REVERT: G 10 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7864 (tm-30) REVERT: G 95 GLN cc_start: 0.8418 (tt0) cc_final: 0.7937 (mm110) REVERT: G 216 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: H 10 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7430 (tp30) REVERT: H 11 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7464 (tm-30) REVERT: H 66 THR cc_start: 0.8690 (m) cc_final: 0.8125 (p) REVERT: I 262 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7389 (tpt170) REVERT: J 236 LYS cc_start: 0.9066 (mttt) cc_final: 0.8835 (mttm) outliers start: 25 outliers final: 14 residues processed: 195 average time/residue: 0.4483 time to fit residues: 95.3143 Evaluate side-chains 192 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103751 restraints weight = 12347.317| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.81 r_work: 0.2954 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11024 Z= 0.150 Angle : 0.510 5.883 15140 Z= 0.289 Chirality : 0.043 0.145 1684 Planarity : 0.004 0.040 1668 Dihedral : 21.588 177.394 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.94 % Allowed : 17.11 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.01 (0.25), residues: 1130 helix: 1.41 (0.23), residues: 494 sheet: -0.16 (0.33), residues: 216 loop : -1.66 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 228 TYR 0.012 0.001 TYR G 194 PHE 0.011 0.001 PHE H 26 TRP 0.015 0.001 TRP B 243 HIS 0.007 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11010) covalent geometry : angle 0.50975 / 0.29 (15138) hydrogen bonds : bond 0.03343 / 2.22 ( 560) hydrogen bonds : angle 4.41066 / 3.07 ( 1550) metal coordination : bond 0.00362 / 0.22 ( 14) metal coordination : angle 0.88567 / 0.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.359 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 10 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7582 (tp30) REVERT: B 11 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 66 THR cc_start: 0.8711 (m) cc_final: 0.8109 (p) REVERT: C 262 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7391 (tpt170) REVERT: G 10 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7933 (tm-30) REVERT: G 95 GLN cc_start: 0.8437 (tt0) cc_final: 0.7966 (mm110) REVERT: G 216 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: H 10 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7408 (tp30) REVERT: H 11 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7499 (tm-30) REVERT: H 13 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7514 (mm-30) REVERT: H 66 THR cc_start: 0.8719 (m) cc_final: 0.8159 (p) REVERT: H 136 LYS cc_start: 0.8222 (tptp) cc_final: 0.7993 (tttm) REVERT: I 262 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7519 (tpt170) REVERT: J 236 LYS cc_start: 0.9105 (mttt) cc_final: 0.8878 (mttm) outliers start: 29 outliers final: 16 residues processed: 201 average time/residue: 0.5028 time to fit residues: 109.6606 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 0.0770 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104812 restraints weight = 12393.864| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.83 r_work: 0.2966 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11024 Z= 0.131 Angle : 0.498 5.859 15140 Z= 0.284 Chirality : 0.043 0.138 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.541 177.945 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.02 % Allowed : 18.42 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.14 (0.25), residues: 1130 helix: 1.55 (0.23), residues: 496 sheet: -0.12 (0.33), residues: 216 loop : -1.60 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 20 TYR 0.010 0.001 TYR G 194 PHE 0.029 0.001 PHE H 26 TRP 0.019 0.001 TRP B 243 HIS 0.004 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (11010) covalent geometry : angle 0.49789 / 0.28 (15138) hydrogen bonds : bond 0.03248 / 2.16 ( 560) hydrogen bonds : angle 4.36842 / 3.04 ( 1550) metal coordination : bond 0.00360 / 0.21 ( 14) metal coordination : angle 0.63883 / 0.36 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.330 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 96 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 10 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7515 (tp30) REVERT: B 11 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 13 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 66 THR cc_start: 0.8704 (m) cc_final: 0.8080 (p) REVERT: C 262 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7380 (tpt170) REVERT: G 10 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7912 (tm-30) REVERT: G 95 GLN cc_start: 0.8378 (tt0) cc_final: 0.7902 (mm110) REVERT: G 216 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: G 242 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8470 (mp) REVERT: H 10 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7411 (tp30) REVERT: H 11 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7458 (tm-30) REVERT: H 13 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7569 (mm-30) REVERT: H 66 THR cc_start: 0.8683 (m) cc_final: 0.8117 (p) REVERT: H 136 LYS cc_start: 0.8169 (tptp) cc_final: 0.7942 (tttm) REVERT: I 262 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7516 (tpt170) REVERT: J 236 LYS cc_start: 0.9062 (mttt) cc_final: 0.8772 (mttp) outliers start: 20 outliers final: 12 residues processed: 194 average time/residue: 0.4608 time to fit residues: 96.9929 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104798 restraints weight = 12342.667| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.83 r_work: 0.2971 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11024 Z= 0.132 Angle : 0.497 6.224 15140 Z= 0.283 Chirality : 0.043 0.139 1684 Planarity : 0.003 0.037 1668 Dihedral : 21.527 178.136 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.33 % Allowed : 19.13 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.28 (0.25), residues: 1130 helix: 1.64 (0.23), residues: 496 sheet: -0.02 (0.33), residues: 216 loop : -1.51 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 263 TYR 0.010 0.001 TYR G 194 PHE 0.032 0.001 PHE H 26 TRP 0.022 0.001 TRP B 243 HIS 0.004 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11010) covalent geometry : angle 0.49712 / 0.28 (15138) hydrogen bonds : bond 0.03203 / 2.13 ( 560) hydrogen bonds : angle 4.32022 / 3.00 ( 1550) metal coordination : bond 0.00346 / 0.20 ( 14) metal coordination : angle 0.72694 / 0.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.366 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 96 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 157 GLU cc_start: 0.8314 (tp30) cc_final: 0.8043 (tp30) REVERT: B 10 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7423 (tp30) REVERT: B 11 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 13 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7089 (tm-30) REVERT: B 66 THR cc_start: 0.8741 (m) cc_final: 0.8093 (p) REVERT: C 262 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7404 (tpt170) REVERT: G 10 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7909 (tm-30) REVERT: G 95 GLN cc_start: 0.8386 (tt0) cc_final: 0.7913 (mm110) REVERT: G 242 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8476 (mp) REVERT: H 10 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7336 (tp30) REVERT: H 11 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7534 (tm-30) REVERT: H 13 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7147 (tm-30) REVERT: H 66 THR cc_start: 0.8679 (m) cc_final: 0.8106 (p) REVERT: H 136 LYS cc_start: 0.8156 (tptp) cc_final: 0.7919 (tttm) REVERT: I 262 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7515 (tpt170) REVERT: J 236 LYS cc_start: 0.9042 (mttt) cc_final: 0.8767 (mttp) REVERT: J 246 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8081 (tt0) outliers start: 23 outliers final: 14 residues processed: 189 average time/residue: 0.4305 time to fit residues: 88.6371 Evaluate side-chains 195 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105184 restraints weight = 12335.715| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.83 r_work: 0.2975 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11024 Z= 0.135 Angle : 0.494 5.869 15140 Z= 0.281 Chirality : 0.043 0.142 1684 Planarity : 0.003 0.036 1668 Dihedral : 21.516 178.190 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.13 % Allowed : 19.43 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.38 (0.25), residues: 1130 helix: 1.73 (0.23), residues: 496 sheet: 0.04 (0.34), residues: 216 loop : -1.47 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 263 TYR 0.010 0.001 TYR A 194 PHE 0.030 0.001 PHE H 26 TRP 0.022 0.001 TRP B 243 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11010) covalent geometry : angle 0.49362 / 0.28 (15138) hydrogen bonds : bond 0.03183 / 2.11 ( 560) hydrogen bonds : angle 4.29680 / 2.99 ( 1550) metal coordination : bond 0.00352 / 0.20 ( 14) metal coordination : angle 0.79521 / 0.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.381 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 96 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 157 GLU cc_start: 0.8295 (tp30) cc_final: 0.8028 (tp30) REVERT: B 10 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7426 (tp30) REVERT: B 11 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 13 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7094 (tm-30) REVERT: B 66 THR cc_start: 0.8754 (m) cc_final: 0.8089 (p) REVERT: C 262 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7020 (tpm170) REVERT: G 10 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7911 (tm-30) REVERT: G 95 GLN cc_start: 0.8395 (tt0) cc_final: 0.7922 (mm110) REVERT: G 242 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8506 (mp) REVERT: H 10 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7329 (tp30) REVERT: H 11 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 13 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7150 (tm-30) REVERT: H 22 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: H 66 THR cc_start: 0.8683 (m) cc_final: 0.8111 (p) REVERT: H 136 LYS cc_start: 0.8183 (tptp) cc_final: 0.7955 (tttm) REVERT: I 262 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7521 (tpt170) REVERT: J 236 LYS cc_start: 0.9052 (mttt) cc_final: 0.8727 (mttt) REVERT: J 246 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8103 (tt0) outliers start: 21 outliers final: 14 residues processed: 189 average time/residue: 0.4536 time to fit residues: 93.4926 Evaluate side-chains 194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101285 restraints weight = 12140.516| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.68 r_work: 0.3051 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11024 Z= 0.135 Angle : 0.496 6.722 15140 Z= 0.282 Chirality : 0.043 0.139 1684 Planarity : 0.003 0.036 1668 Dihedral : 21.503 178.217 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.92 % Allowed : 19.53 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.46 (0.25), residues: 1130 helix: 1.79 (0.23), residues: 496 sheet: 0.09 (0.34), residues: 216 loop : -1.43 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 20 TYR 0.010 0.001 TYR G 194 PHE 0.029 0.001 PHE H 26 TRP 0.023 0.001 TRP B 243 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11010) covalent geometry : angle 0.49571 / 0.28 (15138) hydrogen bonds : bond 0.03181 / 2.11 ( 560) hydrogen bonds : angle 4.28508 / 2.98 ( 1550) metal coordination : bond 0.00352 / 0.20 ( 14) metal coordination : angle 0.71430 / 0.41 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.353 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. REVERT: A 10 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 10 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7398 (tp30) REVERT: B 11 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 13 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7094 (tm-30) REVERT: B 66 THR cc_start: 0.8697 (m) cc_final: 0.8012 (p) REVERT: C 262 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.6999 (tpm170) REVERT: G 10 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7775 (tm-30) REVERT: G 95 GLN cc_start: 0.8250 (tt0) cc_final: 0.7733 (mm110) REVERT: G 242 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8365 (mp) REVERT: H 10 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7281 (tp30) REVERT: H 11 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7507 (tm-30) REVERT: H 13 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7177 (tm-30) REVERT: H 22 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: H 66 THR cc_start: 0.8627 (m) cc_final: 0.8022 (p) REVERT: H 136 LYS cc_start: 0.7999 (tptp) cc_final: 0.7756 (tttm) REVERT: I 262 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7535 (tpt170) REVERT: J 236 LYS cc_start: 0.8881 (mttt) cc_final: 0.8473 (mttt) REVERT: J 246 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7956 (tt0) outliers start: 19 outliers final: 15 residues processed: 191 average time/residue: 0.4618 time to fit residues: 96.4312 Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 262 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100635 restraints weight = 12131.704| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.68 r_work: 0.3044 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11024 Z= 0.148 Angle : 0.503 5.873 15140 Z= 0.285 Chirality : 0.043 0.144 1684 Planarity : 0.003 0.036 1668 Dihedral : 21.522 177.910 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.13 % Allowed : 19.64 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.49 (0.25), residues: 1130 helix: 1.82 (0.23), residues: 496 sheet: 0.11 (0.34), residues: 216 loop : -1.41 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 20 TYR 0.011 0.001 TYR G 194 PHE 0.031 0.001 PHE H 26 TRP 0.025 0.001 TRP B 243 HIS 0.003 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11010) covalent geometry : angle 0.50275 / 0.29 (15138) hydrogen bonds : bond 0.03249 / 2.16 ( 560) hydrogen bonds : angle 4.28686 / 2.98 ( 1550) metal coordination : bond 0.00374 / 0.21 ( 14) metal coordination : angle 0.91573 / 0.51 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.05 seconds wall clock time: 58 minutes 46.98 seconds (3526.98 seconds total)