Starting phenix.real_space_refine on Fri Sep 11 18:29:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6put_20481/09_2026/6put_20481.cif Found real_map, /net/cci-nas-00/data/ceres_data/6put_20481/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6put_20481/09_2026/6put_20481.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6put_20481/09_2026/6put_20481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6put_20481/09_2026/6put_20481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6put_20481/09_2026/6put_20481.map" model { file = "/net/cci-nas-00/data/ceres_data/6put_20481/09_2026/6put_20481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6put_20481/09_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-2.2.1-6174/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: 3.06, per 1000 atoms: 0.28 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: 0.90 Conformation dependent library (CDL) restraints added in 335.6 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: 1.25 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: 1.99 Time building geometry restraints manager: 1.18 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: 14896 2.53 - 5.07: 216 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.090 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- 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 : 0.865 12.664 15140 Z= 0.614 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 0.86371 / 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 : 0.391 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: 0.6095 time to fit residues: 157.3905 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 : 0.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 9 GLN H 216 GLN H 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104402 restraints weight = 12273.198| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.81 r_work: 0.2967 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11024 Z= 0.150 Angle : 0.557 6.301 15140 Z= 0.318 Chirality : 0.045 0.157 1684 Planarity : 0.005 0.047 1668 Dihedral : 21.173 62.162 1976 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.43 % Allowed : 12.96 % Favored : 84.62 % 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: -1.62 (0.22), residues: 1130 helix: -0.20 (0.21), residues: 494 sheet: -0.89 (0.33), residues: 216 loop : -2.14 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 263 TYR 0.011 0.001 TYR H 99 PHE 0.019 0.001 PHE B 26 TRP 0.011 0.001 TRP H 132 HIS 0.004 0.001 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (11010) covalent geometry : angle 0.55596 / 0.32 (15138) hydrogen bonds : bond 0.04018 / 2.66 ( 560) hydrogen bonds : angle 5.01880 / 3.49 ( 1550) metal coordination : bond 0.00657 / 0.32 ( 14) metal coordination : angle 3.45149 / 1.93 ( 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 218 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.401 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: 0.8253 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 242 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 66 THR cc_start: 0.8659 (m) cc_final: 0.8000 (p) REVERT: D 236 LYS cc_start: 0.9041 (mttt) cc_final: 0.8834 (mttt) REVERT: G 10 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7810 (tm-30) REVERT: G 242 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8420 (mp) REVERT: H 66 THR cc_start: 0.8657 (m) cc_final: 0.7996 (p) REVERT: J 236 LYS cc_start: 0.9041 (mttt) cc_final: 0.8835 (mttt) outliers start: 24 outliers final: 4 residues processed: 206 average time/residue: 0.5078 time to fit residues: 113.9968 Evaluate side-chains 178 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR 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: 2.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3565 r_free = 0.3565 target = 0.134548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101970 restraints weight = 12382.718| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.80 r_work: 0.2933 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11024 Z= 0.217 Angle : 0.562 5.780 15140 Z= 0.318 Chirality : 0.046 0.164 1684 Planarity : 0.004 0.043 1668 Dihedral : 21.305 61.413 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.83 % Allowed : 13.16 % Favored : 84.01 % 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: -0.78 (0.24), residues: 1130 helix: 0.63 (0.22), residues: 492 sheet: -0.66 (0.33), residues: 216 loop : -1.77 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 263 TYR 0.016 0.001 TYR A 194 PHE 0.012 0.001 PHE G 185 TRP 0.011 0.002 TRP A 132 HIS 0.004 0.001 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (11010) covalent geometry : angle 0.56183 / 0.32 (15138) hydrogen bonds : bond 0.03964 / 2.65 ( 560) hydrogen bonds : angle 4.74092 / 3.30 ( 1550) metal coordination : bond 0.00644 / 0.31 ( 14) metal coordination : angle 2.30700 / 1.29 ( 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 200 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.425 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: 0.8338 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 242 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 10 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7458 (tp30) REVERT: B 11 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 66 THR cc_start: 0.8687 (m) cc_final: 0.8054 (p) REVERT: C 262 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7047 (tpm170) REVERT: G 10 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 242 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8393 (mp) REVERT: H 10 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7451 (tp30) REVERT: H 11 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7631 (tm-30) REVERT: H 66 THR cc_start: 0.8686 (m) cc_final: 0.8050 (p) REVERT: I 262 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7053 (tpm170) outliers start: 28 outliers final: 14 residues processed: 192 average time/residue: 0.5024 time to fit residues: 105.3991 Evaluate side-chains 190 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN B 252 GLN H 221 GLN H 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103162 restraints weight = 12346.233| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.80 r_work: 0.2940 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1550 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= 0.157 Angle : 0.521 5.873 15140 Z= 0.295 Chirality : 0.044 0.149 1684 Planarity : 0.004 0.041 1668 Dihedral : 21.271 62.414 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 14.17 % Favored : 83.60 % 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: -0.34 (0.24), residues: 1130 helix: 1.10 (0.22), residues: 494 sheet: -0.44 (0.33), residues: 216 loop : -1.71 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 263 TYR 0.012 0.001 TYR G 194 PHE 0.009 0.001 PHE G 185 TRP 0.010 0.001 TRP G 132 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (11010) covalent geometry : angle 0.52038 / 0.30 (15138) hydrogen bonds : bond 0.03526 / 2.35 ( 560) hydrogen bonds : angle 4.53972 / 3.16 ( 1550) metal coordination : bond 0.00336 / 0.16 ( 14) metal coordination : angle 1.44940 / 0.81 ( 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 206 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.396 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: 0.8330 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 242 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 10 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7574 (tp30) REVERT: B 11 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 66 THR cc_start: 0.8711 (m) cc_final: 0.8123 (p) REVERT: C 262 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7007 (tpm170) REVERT: G 10 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 242 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8389 (mp) REVERT: H 10 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7565 (tp30) REVERT: H 11 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7675 (tm-30) REVERT: H 66 THR cc_start: 0.8708 (m) cc_final: 0.8112 (p) REVERT: I 262 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7006 (tpm170) outliers start: 22 outliers final: 10 residues processed: 198 average time/residue: 0.5104 time to fit residues: 110.3893 Evaluate side-chains 190 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 242 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL 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: 0.9990 chunk 55 optimal weight: 0.0000 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.136301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103563 restraints weight = 12325.000| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.82 r_work: 0.2948 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 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 = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1735 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= 0.140 Angle : 0.505 5.843 15140 Z= 0.288 Chirality : 0.043 0.144 1684 Planarity : 0.004 0.041 1668 Dihedral : 21.192 63.025 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 15.59 % 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: -0.02 (0.25), residues: 1130 helix: 1.37 (0.22), residues: 496 sheet: -0.24 (0.34), residues: 216 loop : -1.59 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 263 TYR 0.011 0.001 TYR A 194 PHE 0.009 0.001 PHE A 185 TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11010) covalent geometry : angle 0.50508 / 0.29 (15138) hydrogen bonds : bond 0.03353 / 2.24 ( 560) hydrogen bonds : angle 4.42253 / 3.07 ( 1550) metal coordination : bond 0.00293 / 0.14 ( 14) metal coordination : angle 1.12174 / 0.63 ( 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 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 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: 0.8348 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 242 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 244 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8150 (tmmm) REVERT: B 10 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7529 (tp30) REVERT: B 11 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 66 THR cc_start: 0.8712 (m) cc_final: 0.8126 (p) REVERT: C 262 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7378 (tpt170) REVERT: G 10 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7940 (tm-30) REVERT: G 242 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8394 (mp) REVERT: G 244 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (tmmm) REVERT: H 10 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7519 (tp30) REVERT: H 11 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7713 (tm-30) REVERT: H 66 THR cc_start: 0.8706 (m) cc_final: 0.8113 (p) REVERT: I 262 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7380 (tpt170) outliers start: 22 outliers final: 12 residues processed: 202 average time/residue: 0.4985 time to fit residues: 109.8292 Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LYS 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 242 LEU Chi-restraints excluded: chain G residue 244 LYS 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: 3.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102471 restraints weight = 12373.998| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.83 r_work: 0.2930 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 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: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11024 Z= 0.172 Angle : 0.525 5.797 15140 Z= 0.297 Chirality : 0.044 0.156 1684 Planarity : 0.004 0.040 1668 Dihedral : 21.228 62.599 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.04 % Allowed : 16.80 % Favored : 80.16 % 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: 0.10 (0.25), residues: 1130 helix: 1.47 (0.22), residues: 494 sheet: -0.19 (0.34), residues: 216 loop : -1.50 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 263 TYR 0.013 0.001 TYR A 194 PHE 0.009 0.001 PHE G 185 TRP 0.017 0.001 TRP B 243 HIS 0.003 0.001 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (11010) covalent geometry : angle 0.52524 / 0.30 (15138) hydrogen bonds : bond 0.03442 / 2.29 ( 560) hydrogen bonds : angle 4.42073 / 3.07 ( 1550) metal coordination : bond 0.00331 / 0.16 ( 14) metal coordination : angle 0.99993 / 0.56 ( 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 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.416 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: 0.8350 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 242 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 244 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8156 (tmmm) REVERT: B 10 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7569 (tp30) REVERT: B 66 THR cc_start: 0.8696 (m) cc_final: 0.8072 (p) REVERT: C 262 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7416 (tpt170) REVERT: G 10 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7944 (tm-30) REVERT: G 242 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8390 (mp) REVERT: G 244 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (tmmm) REVERT: H 10 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7583 (tp30) REVERT: H 66 THR cc_start: 0.8690 (m) cc_final: 0.8060 (p) REVERT: I 262 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7417 (tpt170) outliers start: 30 outliers final: 16 residues processed: 200 average time/residue: 0.5228 time to fit residues: 113.8415 Evaluate side-chains 202 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LYS 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 173 LYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 244 LYS 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: 0.7980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102957 restraints weight = 12326.562| |-----------------------------------------------------------------------------| 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: 0.2806 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 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: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1889 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 : 0.516 5.810 15140 Z= 0.292 Chirality : 0.044 0.153 1684 Planarity : 0.004 0.039 1668 Dihedral : 21.206 63.112 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.82 % Allowed : 19.23 % Favored : 78.95 % 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: 0.21 (0.25), residues: 1130 helix: 1.57 (0.22), residues: 496 sheet: -0.13 (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 D 263 TYR 0.012 0.001 TYR A 194 PHE 0.010 0.001 PHE A 185 TRP 0.021 0.001 TRP H 243 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11010) covalent geometry : angle 0.51554 / 0.29 (15138) hydrogen bonds : bond 0.03368 / 2.23 ( 560) hydrogen bonds : angle 4.38642 / 3.05 ( 1550) metal coordination : bond 0.00334 / 0.16 ( 14) metal coordination : angle 1.00184 / 0.56 ( 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: 18 poor density : 184 time to evaluate : 0.323 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: 0.8343 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 242 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 244 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8166 (tmmm) REVERT: B 10 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7597 (tp30) REVERT: B 11 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 66 THR cc_start: 0.8709 (m) cc_final: 0.8081 (p) REVERT: C 262 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7414 (tpt170) REVERT: G 10 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7940 (tm-30) REVERT: G 242 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8413 (mp) REVERT: G 244 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8160 (tmmm) REVERT: H 10 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7601 (tp30) REVERT: H 11 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7684 (tm-30) REVERT: H 66 THR cc_start: 0.8709 (m) cc_final: 0.8074 (p) REVERT: I 262 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7412 (tpt170) outliers start: 18 outliers final: 10 residues processed: 198 average time/residue: 0.5111 time to fit residues: 110.4926 Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LYS 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 242 LEU Chi-restraints excluded: chain G residue 244 LYS 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: 0.6980 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.136877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104392 restraints weight = 12327.163| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.83 r_work: 0.2964 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 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 = 0.2834 r_free = 0.2834 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: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1939 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= 0.124 Angle : 0.505 5.863 15140 Z= 0.286 Chirality : 0.043 0.149 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.128 64.173 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.82 % Allowed : 20.14 % Favored : 78.04 % 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: -0.05 (0.34), residues: 216 loop : -1.42 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 228 TYR 0.009 0.001 TYR A 194 PHE 0.007 0.001 PHE A 185 TRP 0.022 0.001 TRP B 243 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11010) covalent geometry : angle 0.50463 / 0.29 (15138) hydrogen bonds : bond 0.03198 / 2.12 ( 560) hydrogen bonds : angle 4.31585 / 3.00 ( 1550) metal coordination : bond 0.00233 / 0.11 ( 14) metal coordination : angle 0.73656 / 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 203 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.431 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: 0.8361 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 96 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 244 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8163 (tmmm) REVERT: B 10 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7540 (tp30) REVERT: B 11 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 66 THR cc_start: 0.8699 (m) cc_final: 0.8063 (p) REVERT: C 262 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7405 (tpt170) REVERT: G 10 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7949 (tm-30) REVERT: G 96 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7529 (mm-30) REVERT: G 244 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8160 (tmmm) REVERT: H 10 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7518 (tp30) REVERT: H 11 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7674 (tm-30) REVERT: H 66 THR cc_start: 0.8690 (m) cc_final: 0.8045 (p) REVERT: I 262 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7397 (tpt170) outliers start: 18 outliers final: 12 residues processed: 195 average time/residue: 0.4700 time to fit residues: 100.0476 Evaluate side-chains 199 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 244 LYS 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 244 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL 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: 1.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.135425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102914 restraints weight = 12324.811| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.82 r_work: 0.2935 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 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: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11024 Z= 0.168 Angle : 0.515 5.831 15140 Z= 0.292 Chirality : 0.044 0.154 1684 Planarity : 0.004 0.038 1668 Dihedral : 21.172 63.113 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 19.64 % Favored : 78.14 % 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: 0.40 (0.25), residues: 1130 helix: 1.74 (0.22), residues: 496 sheet: -0.04 (0.34), residues: 216 loop : -1.39 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 231 TYR 0.012 0.001 TYR A 194 PHE 0.011 0.001 PHE A 185 TRP 0.024 0.001 TRP B 243 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (11010) covalent geometry : angle 0.51536 / 0.29 (15138) hydrogen bonds : bond 0.03339 / 2.22 ( 560) hydrogen bonds : angle 4.32501 / 3.01 ( 1550) metal coordination : bond 0.00337 / 0.16 ( 14) metal coordination : angle 1.01307 / 0.57 ( 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 208 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.327 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: 0.7935 (tm-30) REVERT: A 96 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 244 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8166 (tmmm) REVERT: B 10 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7538 (tp30) REVERT: B 11 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 13 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7139 (tm-30) REVERT: B 66 THR cc_start: 0.8760 (m) cc_final: 0.8081 (p) REVERT: C 262 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7421 (tpt170) REVERT: G 10 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7951 (tm-30) REVERT: G 96 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7508 (mm-30) REVERT: G 244 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (tmmm) REVERT: H 10 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7493 (tp30) REVERT: H 11 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7672 (tm-30) REVERT: H 13 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7136 (tm-30) REVERT: H 66 THR cc_start: 0.8762 (m) cc_final: 0.8078 (p) REVERT: I 262 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7424 (tpt170) outliers start: 22 outliers final: 14 residues processed: 200 average time/residue: 0.4946 time to fit residues: 108.0793 Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 244 LYS 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 244 LYS 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: 3.9990 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.135118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102604 restraints weight = 12287.253| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.82 r_work: 0.2931 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 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: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11024 Z= 0.174 Angle : 0.532 6.761 15140 Z= 0.300 Chirality : 0.044 0.160 1684 Planarity : 0.004 0.038 1668 Dihedral : 21.205 63.311 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.82 % Allowed : 20.24 % Favored : 77.94 % 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 (0.22), residues: 494 sheet: 0.00 (0.33), residues: 216 loop : -1.35 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 20 TYR 0.012 0.001 TYR G 194 PHE 0.018 0.001 PHE B 26 TRP 0.026 0.002 TRP H 243 HIS 0.004 0.001 HIS H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11010) covalent geometry : angle 0.53189 / 0.30 (15138) hydrogen bonds : bond 0.03379 / 2.24 ( 560) hydrogen bonds : angle 4.34465 / 3.02 ( 1550) metal coordination : bond 0.00358 / 0.17 ( 14) metal coordination : angle 0.99204 / 0.55 ( 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 205 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.437 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: 0.8338 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 219 LYS cc_start: 0.8204 (ptmm) cc_final: 0.7850 (ptmt) REVERT: A 244 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8177 (tmmm) REVERT: B 10 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7541 (tp30) REVERT: B 11 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 13 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7255 (tm-30) REVERT: B 66 THR cc_start: 0.8761 (m) cc_final: 0.8072 (p) REVERT: C 262 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7426 (tpt170) REVERT: G 10 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7951 (tm-30) REVERT: G 219 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7853 (ptmt) REVERT: G 244 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8179 (tmmm) REVERT: H 10 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7555 (tp30) REVERT: H 11 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7674 (tm-30) REVERT: H 13 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7193 (tm-30) REVERT: H 66 THR cc_start: 0.8763 (m) cc_final: 0.8070 (p) REVERT: I 262 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7433 (tpt170) outliers start: 18 outliers final: 14 residues processed: 197 average time/residue: 0.5335 time to fit residues: 114.6531 Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 244 LYS 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 244 LYS 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: 0.6980 chunk 27 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.0170 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.136269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104268 restraints weight = 12246.535| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.82 r_work: 0.2956 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 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 = 0.2828 r_free = 0.2828 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: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11024 Z= 0.122 Angle : 0.513 6.708 15140 Z= 0.290 Chirality : 0.043 0.156 1684 Planarity : 0.004 0.038 1668 Dihedral : 21.149 64.418 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.82 % Allowed : 19.84 % Favored : 78.34 % 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: 0.57 (0.25), residues: 1130 helix: 1.91 (0.22), residues: 494 sheet: 0.00 (0.34), residues: 216 loop : -1.30 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.010 0.001 TYR G 194 PHE 0.007 0.001 PHE G 185 TRP 0.029 0.002 TRP H 243 HIS 0.002 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (11010) covalent geometry : angle 0.51309 / 0.29 (15138) hydrogen bonds : bond 0.03211 / 2.13 ( 560) hydrogen bonds : angle 4.29618 / 2.99 ( 1550) metal coordination : bond 0.00263 / 0.13 ( 14) metal coordination : angle 1.08103 / 0.60 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3943.95 seconds wall clock time: 68 minutes 3.19 seconds (4083.19 seconds total)