Starting phenix.real_space_refine on Sat Sep 12 17:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.map" model { file = "/net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6voy_21301/09_2026/6voy_21301.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Zn 4 6.06 5 P 178 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 10706 2.51 5 N 3072 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 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: 17556 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "J" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "K" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "M" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "N" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 246 SG CYS A 33 63.285 78.778 64.823 1.00116.78 S ATOM 267 SG CYS A 36 64.894 75.597 65.874 1.00 99.36 S ATOM 2439 SG CYS B 33 137.488 80.123 80.291 1.00299.42 S ATOM 2460 SG CYS B 36 138.441 77.611 78.802 1.00269.90 S ATOM 4504 SG CYS C 33 105.877 38.294 66.337 1.00107.32 S ATOM 4525 SG CYS C 36 104.269 41.389 64.821 1.00 95.45 S ATOM 6697 SG CYS D 33 31.902 36.894 81.648 1.00337.40 S ATOM 6718 SG CYS D 36 30.371 38.588 79.947 1.00308.22 S Time building chain proxies: 3.97, per 1000 atoms: 0.23 Number of scatterers: 17556 At special positions: 0 Unit cell: (170.62, 115.236, 139.355, 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 S 54 16.00 P 178 15.00 Mg 2 11.99 O 3540 8.00 N 3072 7.00 C 10706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 647.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 10 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 6 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 10 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 6 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 36 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 6 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 10 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 36 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 10 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 6 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 36 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 33 " Number of angles added : 7 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 51.7% alpha, 4.1% beta 82 base pairs and 123 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 171 Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 148 through 151 Processing helix chain 'C' and resid 152 through 172 Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 171 Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 63 through 83 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 175 through 193 Processing helix chain 'E' and resid 194 through 213 Processing helix chain 'E' and resid 221 through 234 Processing helix chain 'E' and resid 241 through 251 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 277 through 286 Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 298 through 310 Processing helix chain 'E' and resid 320 through 332 removed outlier: 4.731A pdb=" N GLU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) Proline residue: E 326 - end of helix removed outlier: 3.696A pdb=" N GLN E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 83 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 170 through 173 Processing helix chain 'F' and resid 175 through 193 Processing helix chain 'F' and resid 194 through 213 Processing helix chain 'F' and resid 221 through 234 Processing helix chain 'F' and resid 241 through 251 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 277 through 286 Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 298 through 310 Processing helix chain 'F' and resid 320 through 332 removed outlier: 4.702A pdb=" N GLU F 325 " --> pdb=" O VAL F 321 " (cutoff:3.500A) Proline residue: F 326 - end of helix removed outlier: 3.701A pdb=" N GLN F 330 " --> pdb=" O PRO F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 353 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 230 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'B' and resid 228 through 230 removed outlier: 4.195A pdb=" N GLN B 244 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 230 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY B 242 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 65 Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 117 589 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 123 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3018 1.32 - 1.45: 5935 1.45 - 1.58: 9006 1.58 - 1.70: 347 1.70 - 1.83: 80 Bond restraints: 18386 Sorted by residual: bond pdb=" C3' DG L 46 " pdb=" C2' DG L 46 " ideal model delta sigma weight residual 1.516 1.568 -0.052 8.00e-03 1.56e+04 4.19e+01 bond pdb=" N3 DA I 21 " pdb=" C4 DA I 21 " ideal model delta sigma weight residual 1.344 1.311 0.033 6.00e-03 2.78e+04 2.95e+01 bond pdb=" N3 DA L 21 " pdb=" C4 DA L 21 " ideal model delta sigma weight residual 1.344 1.312 0.032 6.00e-03 2.78e+04 2.89e+01 bond pdb=" C3' DT K 7 " pdb=" C2' DT K 7 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.81e+01 bond pdb=" C3' DG J 6 " pdb=" O3' DG J 6 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.49e+01 ... (remaining 18381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.35: 25588 6.35 - 12.71: 159 12.71 - 19.06: 15 19.06 - 25.41: 3 25.41 - 31.77: 3 Bond angle restraints: 25768 Sorted by residual: angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " ideal model delta sigma weight residual 110.63 78.86 31.77 1.94e+00 2.66e-01 2.68e+02 angle pdb=" C TRP D 227 " pdb=" N TYR D 228 " pdb=" CA TYR D 228 " ideal model delta sigma weight residual 121.70 150.62 -28.92 1.80e+00 3.09e-01 2.58e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" C PHE C 230 " ideal model delta sigma weight residual 112.12 132.09 -19.97 1.34e+00 5.57e-01 2.22e+02 angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" C PHE A 230 " ideal model delta sigma weight residual 112.12 131.73 -19.61 1.34e+00 5.57e-01 2.14e+02 angle pdb=" O4' DC K 11 " pdb=" C1' DC K 11 " pdb=" N1 DC K 11 " ideal model delta sigma weight residual 108.00 117.88 -9.88 7.00e-01 2.04e+00 1.99e+02 ... (remaining 25763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 9409 35.22 - 70.43: 1023 70.43 - 105.65: 52 105.65 - 140.86: 5 140.86 - 176.08: 9 Dihedral angle restraints: 10498 sinusoidal: 5394 harmonic: 5104 Sorted by residual: dihedral pdb=" CA GLU E 276 " pdb=" C GLU E 276 " pdb=" N LYS E 277 " pdb=" CA LYS E 277 " ideal model delta harmonic sigma weight residual -180.00 -49.46 -130.54 0 5.00e+00 4.00e-02 6.82e+02 dihedral pdb=" CA GLU F 276 " pdb=" C GLU F 276 " pdb=" N LYS F 277 " pdb=" CA LYS F 277 " ideal model delta harmonic sigma weight residual -180.00 -50.02 -129.98 0 5.00e+00 4.00e-02 6.76e+02 dihedral pdb=" CA GLN A 244 " pdb=" C GLN A 244 " pdb=" N GLU A 245 " pdb=" CA GLU A 245 " ideal model delta harmonic sigma weight residual -180.00 -83.94 -96.06 0 5.00e+00 4.00e-02 3.69e+02 ... (remaining 10495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2853 0.336 - 0.672: 23 0.672 - 1.009: 4 1.009 - 1.345: 1 1.345 - 1.681: 1 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA TYR D 228 " pdb=" N TYR D 228 " pdb=" C TYR D 228 " pdb=" CB TYR D 228 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" CA PRO C 243 " pdb=" N PRO C 243 " pdb=" C PRO C 243 " pdb=" CB PRO C 243 " both_signs ideal model delta sigma weight residual False 2.72 1.71 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA PRO A 243 " pdb=" N PRO A 243 " pdb=" C PRO A 243 " pdb=" CB PRO A 243 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 2879 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 153 " 0.043 2.00e-02 2.50e+03 8.63e-02 7.45e+01 pdb=" C GLY B 153 " -0.149 2.00e-02 2.50e+03 pdb=" O GLY B 153 " 0.056 2.00e-02 2.50e+03 pdb=" N LEU B 154 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 132 " -0.041 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C PRO F 132 " 0.138 2.00e-02 2.50e+03 pdb=" O PRO F 132 " -0.051 2.00e-02 2.50e+03 pdb=" N HIS F 133 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 132 " 0.041 2.00e-02 2.50e+03 8.00e-02 6.39e+01 pdb=" C PRO E 132 " -0.138 2.00e-02 2.50e+03 pdb=" O PRO E 132 " 0.051 2.00e-02 2.50e+03 pdb=" N HIS E 133 " 0.047 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 47 2.25 - 2.91: 8538 2.91 - 3.57: 28016 3.57 - 4.24: 42570 4.24 - 4.90: 62808 Nonbonded interactions: 141979 Sorted by model distance: nonbonded pdb=" O TRP A 60 " pdb=" O VAL A 80 " model vdw 1.583 3.040 nonbonded pdb=" CD2 HIS B 6 " pdb=" CD2 HIS B 10 " model vdw 1.769 3.480 nonbonded pdb=" O GLY C 122 " pdb=" N TYR C 125 " model vdw 1.971 3.120 nonbonded pdb=" OD2 ASP A 63 " pdb="MG MG A 302 " model vdw 1.992 2.170 nonbonded pdb=" NE2 GLN A 44 " pdb=" OP1 DT J 10 " model vdw 2.005 3.120 ... (remaining 141974 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 37 or resid 53 through 274)) selection = (chain 'B' and resid 1 through 274) selection = (chain 'C' and (resid 1 through 37 or resid 53 through 274)) selection = (chain 'D' and resid 1 through 274) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.220 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.013 0.379 18402 Z= 0.853 Angle : 1.616 43.689 25775 Z= 1.036 Chirality : 0.101 1.681 2882 Planarity : 0.013 0.095 2630 Dihedral : 24.618 176.075 7174 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 34.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.46 % Allowed : 13.41 % Favored : 86.12 % Cbeta Deviations : 1.81 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.96 % Twisted General : 1.49 % 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: -6.32 (0.14), residues: 1700 helix: -4.02 (0.11), residues: 784 sheet: -3.45 (0.47), residues: 100 loop : -4.53 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 51 TYR 0.058 0.004 TYR D 228 PHE 0.031 0.003 PHE A 230 TRP 0.043 0.004 TRP A 227 HIS 0.052 0.003 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.01271 / 0.85 (18386) covalent geometry : angle 1.56024 / 1.03 (25768) hydrogen bonds : bond 0.15093 / 10.29 ( 787) hydrogen bonds : angle 8.18449 / 5.80 ( 2045) metal coordination : bond 0.13404 / 7.18 ( 16) metal coordination : angle 25.50425 / 15.16 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 433 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.9000 (p0) cc_final: 0.8453 (p0) REVERT: A 179 ASP cc_start: 0.8924 (p0) cc_final: 0.8462 (p0) REVERT: A 238 ARG cc_start: 0.8415 (tpm170) cc_final: 0.8169 (mmm160) REVERT: A 248 GLN cc_start: 0.8186 (tp40) cc_final: 0.7964 (tm-30) REVERT: A 249 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 129 ASP cc_start: 0.9192 (m-30) cc_final: 0.8847 (m-30) REVERT: B 241 LYS cc_start: 0.9315 (mppt) cc_final: 0.8818 (mtmm) REVERT: C 133 MET cc_start: 0.8332 (tpp) cc_final: 0.8113 (tpp) REVERT: C 173 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8728 (mtpp) REVERT: C 175 ASP cc_start: 0.8880 (p0) cc_final: 0.8493 (p0) REVERT: D 99 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8752 (mm-30) REVERT: D 111 LEU cc_start: 0.7730 (mt) cc_final: 0.7509 (mt) REVERT: D 175 ASP cc_start: 0.9008 (p0) cc_final: 0.8694 (p0) REVERT: E 141 PHE cc_start: 0.9401 (t80) cc_final: 0.9067 (t80) REVERT: E 143 ARG cc_start: 0.8673 (tmt170) cc_final: 0.8287 (tmt170) REVERT: E 183 LYS cc_start: 0.9509 (ttmt) cc_final: 0.9215 (ttmt) REVERT: E 223 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: E 226 GLU cc_start: 0.9417 (mp0) cc_final: 0.9044 (mp0) REVERT: F 183 LYS cc_start: 0.9382 (ttmt) cc_final: 0.8905 (ttmt) REVERT: F 223 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: F 226 GLU cc_start: 0.9314 (mp0) cc_final: 0.8967 (mp0) outliers start: 7 outliers final: 0 residues processed: 437 average time/residue: 0.1449 time to fit residues: 94.3237 Evaluate side-chains 372 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain F residue 223 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 128 GLN A 132 ASN A 141 HIS A 156 GLN A 204 GLN A 224 GLN A 226 HIS B 34 HIS B 193 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 141 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 226 HIS D 61 GLN D 77 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS E 205 ASN E 233 ASN E 306 ASN F 85 ASN F 187 HIS F 205 ASN F 233 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.178096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122152 restraints weight = 37793.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125622 restraints weight = 17523.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127705 restraints weight = 11480.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128865 restraints weight = 9094.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129420 restraints weight = 8106.822| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 18402 Z= 0.271 Angle : 1.052 25.145 25775 Z= 0.559 Chirality : 0.059 0.513 2882 Planarity : 0.007 0.064 2630 Dihedral : 28.478 179.993 3850 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.00 % Favored : 85.47 % Rotamer: Outliers : 2.99 % Allowed : 21.12 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 1.00 % 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: -4.33 (0.18), residues: 1700 helix: -2.07 (0.16), residues: 754 sheet: -2.71 (0.45), residues: 112 loop : -3.77 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 201 TYR 0.035 0.003 TYR E 209 PHE 0.024 0.003 PHE B 170 TRP 0.032 0.003 TRP E 131 HIS 0.015 0.002 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.27 (18386) covalent geometry : angle 1.03098 / 0.56 (25768) hydrogen bonds : bond 0.09701 / 6.56 ( 787) hydrogen bonds : angle 6.62386 / 4.71 ( 2045) metal coordination : bond 0.03750 / 2.70 ( 16) metal coordination : angle 12.65904 / 8.16 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 414 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8595 (pp30) cc_final: 0.8186 (pp30) REVERT: A 106 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 175 ASP cc_start: 0.8867 (p0) cc_final: 0.8367 (p0) REVERT: A 179 ASP cc_start: 0.8793 (p0) cc_final: 0.8277 (p0) REVERT: A 245 GLU cc_start: 0.8562 (pm20) cc_final: 0.8342 (pm20) REVERT: A 249 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 113 LYS cc_start: 0.7603 (tmtt) cc_final: 0.7368 (tptp) REVERT: B 229 TYR cc_start: 0.8692 (m-10) cc_final: 0.8128 (m-10) REVERT: B 241 LYS cc_start: 0.9285 (mppt) cc_final: 0.9058 (mppt) REVERT: B 245 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 133 MET cc_start: 0.8176 (tpp) cc_final: 0.7939 (tpp) REVERT: C 172 ASP cc_start: 0.8454 (t0) cc_final: 0.8184 (t0) REVERT: C 173 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8744 (mtpp) REVERT: C 175 ASP cc_start: 0.8778 (p0) cc_final: 0.8392 (p0) REVERT: C 186 LEU cc_start: 0.9395 (tt) cc_final: 0.9179 (tp) REVERT: D 99 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8719 (mm-30) REVERT: D 116 TYR cc_start: 0.8490 (m-80) cc_final: 0.8250 (m-80) REVERT: D 165 LEU cc_start: 0.9417 (tp) cc_final: 0.9195 (tp) REVERT: E 70 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8301 (tpp-160) REVERT: E 87 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5559 (mt) REVERT: E 103 MET cc_start: 0.8567 (pmm) cc_final: 0.8298 (pmm) REVERT: E 136 LEU cc_start: 0.9357 (mt) cc_final: 0.9148 (mt) REVERT: E 141 PHE cc_start: 0.9263 (t80) cc_final: 0.8973 (t80) REVERT: E 203 GLN cc_start: 0.9484 (tp-100) cc_final: 0.9172 (mm-40) REVERT: E 307 GLU cc_start: 0.9063 (tp30) cc_final: 0.8709 (tp30) REVERT: F 70 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8269 (tpp-160) REVERT: F 87 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5768 (mt) REVERT: F 103 MET cc_start: 0.8594 (pmm) cc_final: 0.8366 (pmm) REVERT: F 131 TRP cc_start: 0.7857 (t-100) cc_final: 0.7640 (t-100) REVERT: F 203 GLN cc_start: 0.9485 (tp-100) cc_final: 0.9164 (mm-40) REVERT: F 307 GLU cc_start: 0.9127 (tp30) cc_final: 0.8767 (tp30) outliers start: 45 outliers final: 31 residues processed: 432 average time/residue: 0.1334 time to fit residues: 88.2214 Evaluate side-chains 418 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 385 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 268 TRP Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 270 CYS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 132 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 199 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 226 HIS E 48 GLN E 82 HIS E 206 ASN F 38 GLN F 82 HIS F 187 HIS F 206 ASN F 306 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.176726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121292 restraints weight = 37886.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124795 restraints weight = 16782.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126957 restraints weight = 10815.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128141 restraints weight = 8506.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128691 restraints weight = 7495.585| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 18402 Z= 0.255 Angle : 0.951 19.517 25775 Z= 0.510 Chirality : 0.056 0.453 2882 Planarity : 0.006 0.046 2630 Dihedral : 28.248 178.198 3844 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.94 % Favored : 86.65 % Rotamer: Outliers : 5.64 % Allowed : 22.64 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -3.55 (0.19), residues: 1700 helix: -1.09 (0.18), residues: 756 sheet: -2.49 (0.45), residues: 108 loop : -3.69 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 218 TYR 0.037 0.003 TYR E 209 PHE 0.021 0.002 PHE E 99 TRP 0.048 0.003 TRP A 268 HIS 0.011 0.002 HIS C 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (18386) covalent geometry : angle 0.93945 / 0.51 (25768) hydrogen bonds : bond 0.08355 / 5.64 ( 787) hydrogen bonds : angle 6.10583 / 4.32 ( 2045) metal coordination : bond 0.02868 / 1.94 ( 16) metal coordination : angle 8.91043 / 6.09 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 396 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8740 (pp30) cc_final: 0.8439 (pp30) REVERT: A 75 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7618 (mtt90) REVERT: A 106 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 175 ASP cc_start: 0.8858 (p0) cc_final: 0.8480 (p0) REVERT: A 179 ASP cc_start: 0.8766 (p0) cc_final: 0.8160 (p0) REVERT: A 245 GLU cc_start: 0.8710 (pm20) cc_final: 0.8449 (pm20) REVERT: B 128 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: B 139 ILE cc_start: 0.9440 (mm) cc_final: 0.9210 (mm) REVERT: B 178 MET cc_start: 0.7810 (mpp) cc_final: 0.7182 (tpp) REVERT: B 229 TYR cc_start: 0.8772 (m-10) cc_final: 0.8206 (m-10) REVERT: B 241 LYS cc_start: 0.9296 (mppt) cc_final: 0.8808 (mtmm) REVERT: C 13 GLN cc_start: 0.8909 (pm20) cc_final: 0.8444 (pp30) REVERT: C 63 ASP cc_start: 0.8093 (t0) cc_final: 0.7791 (t0) REVERT: C 133 MET cc_start: 0.8218 (tpp) cc_final: 0.8002 (tpp) REVERT: C 172 ASP cc_start: 0.8514 (t0) cc_final: 0.8191 (p0) REVERT: C 173 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8532 (mtpp) REVERT: C 175 ASP cc_start: 0.8805 (p0) cc_final: 0.8416 (p0) REVERT: C 199 HIS cc_start: 0.8580 (m-70) cc_final: 0.8374 (m-70) REVERT: D 99 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8765 (mm-30) REVERT: D 116 TYR cc_start: 0.8582 (m-80) cc_final: 0.8334 (m-80) REVERT: D 165 LEU cc_start: 0.9341 (tp) cc_final: 0.9069 (tt) REVERT: E 70 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8479 (tpp-160) REVERT: E 87 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5847 (mt) REVERT: E 141 PHE cc_start: 0.9285 (t80) cc_final: 0.8946 (t80) REVERT: E 183 LYS cc_start: 0.9411 (ttpt) cc_final: 0.9116 (ttpt) REVERT: E 226 GLU cc_start: 0.9309 (mp0) cc_final: 0.9097 (mp0) REVERT: E 320 PHE cc_start: 0.6754 (t80) cc_final: 0.6530 (t80) REVERT: F 87 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.5975 (mt) REVERT: F 178 GLU cc_start: 0.9192 (pp20) cc_final: 0.8988 (pp20) outliers start: 85 outliers final: 51 residues processed: 436 average time/residue: 0.1345 time to fit residues: 89.0582 Evaluate side-chains 431 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 377 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 268 TRP Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 66 optimal weight: 0.0770 chunk 52 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN E 82 HIS F 38 GLN F 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123447 restraints weight = 38062.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127086 restraints weight = 17165.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129295 restraints weight = 11151.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130527 restraints weight = 8829.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131144 restraints weight = 7814.206| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18402 Z= 0.191 Angle : 0.887 15.741 25775 Z= 0.474 Chirality : 0.054 0.411 2882 Planarity : 0.005 0.046 2630 Dihedral : 27.998 177.205 3844 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.82 % Favored : 87.82 % Rotamer: Outliers : 6.04 % Allowed : 24.63 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -3.18 (0.19), residues: 1700 helix: -0.80 (0.18), residues: 774 sheet: -2.30 (0.45), residues: 108 loop : -3.52 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 218 TYR 0.024 0.002 TYR D 228 PHE 0.028 0.002 PHE B 170 TRP 0.043 0.002 TRP A 268 HIS 0.010 0.001 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (18386) covalent geometry : angle 0.87981 / 0.47 (25768) hydrogen bonds : bond 0.07349 / 4.95 ( 787) hydrogen bonds : angle 5.78943 / 4.08 ( 2045) metal coordination : bond 0.02211 / 1.59 ( 16) metal coordination : angle 6.86935 / 4.56 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 424 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8920 (pp20) cc_final: 0.8635 (pp20) REVERT: A 106 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 148 ASN cc_start: 0.9336 (t0) cc_final: 0.8902 (t0) REVERT: A 175 ASP cc_start: 0.8797 (p0) cc_final: 0.8442 (p0) REVERT: A 179 ASP cc_start: 0.8684 (p0) cc_final: 0.8040 (p0) REVERT: B 119 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6596 (t) REVERT: B 128 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: B 178 MET cc_start: 0.7788 (mpp) cc_final: 0.6909 (tpp) REVERT: B 229 TYR cc_start: 0.8720 (m-10) cc_final: 0.8185 (m-10) REVERT: B 241 LYS cc_start: 0.9310 (mppt) cc_final: 0.9093 (mppt) REVERT: C 51 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7047 (pmt-80) REVERT: C 63 ASP cc_start: 0.8144 (t0) cc_final: 0.7886 (t0) REVERT: C 106 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8544 (tm-30) REVERT: C 133 MET cc_start: 0.8178 (tpp) cc_final: 0.7973 (tpp) REVERT: C 148 ASN cc_start: 0.9405 (t0) cc_final: 0.8955 (t0) REVERT: C 172 ASP cc_start: 0.8464 (t0) cc_final: 0.8171 (t0) REVERT: C 173 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8619 (mtpp) REVERT: C 175 ASP cc_start: 0.8715 (p0) cc_final: 0.8335 (p0) REVERT: C 199 HIS cc_start: 0.8535 (m-70) cc_final: 0.8296 (m-70) REVERT: C 238 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.5801 (mmm160) REVERT: C 249 GLU cc_start: 0.8599 (tp30) cc_final: 0.8219 (tp30) REVERT: D 99 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8735 (mm-30) REVERT: D 116 TYR cc_start: 0.8559 (m-80) cc_final: 0.8303 (m-80) REVERT: D 165 LEU cc_start: 0.9337 (tp) cc_final: 0.9092 (tt) REVERT: D 200 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8875 (mmmm) REVERT: D 226 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: E 67 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: E 70 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8467 (tpt170) REVERT: E 87 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5520 (mt) REVERT: E 141 PHE cc_start: 0.9299 (t80) cc_final: 0.8872 (t80) REVERT: E 203 GLN cc_start: 0.9490 (tp-100) cc_final: 0.9068 (mm-40) REVERT: E 263 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8409 (p90) REVERT: E 266 GLN cc_start: 0.8249 (pm20) cc_final: 0.8006 (pm20) REVERT: E 267 LEU cc_start: 0.9021 (pp) cc_final: 0.8271 (pp) REVERT: F 67 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: F 70 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8067 (tpp-160) REVERT: F 87 ILE cc_start: 0.6322 (OUTLIER) cc_final: 0.5913 (mt) REVERT: F 203 GLN cc_start: 0.9495 (tp-100) cc_final: 0.9074 (mm-40) outliers start: 91 outliers final: 51 residues processed: 467 average time/residue: 0.1288 time to fit residues: 91.9550 Evaluate side-chains 463 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 402 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS E 264 HIS F 38 GLN F 82 HIS F 233 ASN F 243 HIS F 264 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124646 restraints weight = 37640.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128319 restraints weight = 16915.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130518 restraints weight = 10881.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131688 restraints weight = 8572.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132400 restraints weight = 7580.855| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18402 Z= 0.183 Angle : 0.875 14.228 25775 Z= 0.463 Chirality : 0.053 0.371 2882 Planarity : 0.005 0.042 2630 Dihedral : 27.830 176.433 3844 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.12 % Favored : 87.65 % Rotamer: Outliers : 6.51 % Allowed : 26.56 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.20), residues: 1700 helix: -0.50 (0.18), residues: 774 sheet: -2.11 (0.47), residues: 108 loop : -3.40 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 218 TYR 0.023 0.002 TYR D 228 PHE 0.025 0.002 PHE B 170 TRP 0.033 0.003 TRP C 268 HIS 0.009 0.001 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (18386) covalent geometry : angle 0.87034 / 0.46 (25768) hydrogen bonds : bond 0.06852 / 4.60 ( 787) hydrogen bonds : angle 5.63603 / 3.96 ( 2045) metal coordination : bond 0.01895 / 1.37 ( 16) metal coordination : angle 5.48832 / 3.63 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 423 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.6013 (m-70) cc_final: 0.5790 (m90) REVERT: A 106 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 148 ASN cc_start: 0.9337 (t0) cc_final: 0.8930 (t0) REVERT: A 175 ASP cc_start: 0.8752 (p0) cc_final: 0.8389 (p0) REVERT: A 179 ASP cc_start: 0.8665 (p0) cc_final: 0.8109 (p0) REVERT: B 119 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6664 (t) REVERT: B 128 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: B 170 PHE cc_start: 0.8513 (p90) cc_final: 0.8111 (p90) REVERT: B 172 ASP cc_start: 0.9047 (t70) cc_final: 0.8324 (t0) REVERT: B 178 MET cc_start: 0.7852 (mpp) cc_final: 0.6795 (tpp) REVERT: B 229 TYR cc_start: 0.8732 (m-10) cc_final: 0.8178 (m-10) REVERT: B 241 LYS cc_start: 0.9302 (mppt) cc_final: 0.9082 (mppt) REVERT: C 63 ASP cc_start: 0.8125 (t0) cc_final: 0.7891 (t0) REVERT: C 106 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8554 (tm-30) REVERT: C 133 MET cc_start: 0.8199 (tpp) cc_final: 0.7991 (tpp) REVERT: C 148 ASN cc_start: 0.9404 (t0) cc_final: 0.8933 (t0) REVERT: C 175 ASP cc_start: 0.8650 (p0) cc_final: 0.8253 (p0) REVERT: C 178 MET cc_start: 0.7884 (tpp) cc_final: 0.7670 (tpp) REVERT: C 199 HIS cc_start: 0.8531 (m-70) cc_final: 0.8304 (m-70) REVERT: C 238 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.5829 (mmm160) REVERT: D 99 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8692 (mm-30) REVERT: D 116 TYR cc_start: 0.8577 (m-80) cc_final: 0.8276 (m-80) REVERT: D 165 LEU cc_start: 0.9376 (tp) cc_final: 0.9141 (tt) REVERT: D 200 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8866 (mmmm) REVERT: D 226 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.6039 (m-70) REVERT: E 39 GLU cc_start: 0.7591 (pm20) cc_final: 0.7354 (pm20) REVERT: E 70 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8381 (tpt170) REVERT: E 87 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5590 (mt) REVERT: E 225 LEU cc_start: 0.9122 (mp) cc_final: 0.8810 (mp) REVERT: E 263 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8430 (p90) REVERT: E 266 GLN cc_start: 0.8254 (pm20) cc_final: 0.7892 (pm20) REVERT: E 267 LEU cc_start: 0.8927 (pp) cc_final: 0.8146 (pp) REVERT: F 67 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: F 70 ARG cc_start: 0.8595 (tpp-160) cc_final: 0.8165 (tpp-160) REVERT: F 76 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8822 (ptp) REVERT: F 87 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5758 (mt) REVERT: F 175 ASP cc_start: 0.8029 (t0) cc_final: 0.7797 (t0) REVERT: F 203 GLN cc_start: 0.9451 (tp-100) cc_final: 0.8973 (mm-40) outliers start: 98 outliers final: 58 residues processed: 470 average time/residue: 0.1294 time to fit residues: 93.4020 Evaluate side-chains 464 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 397 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 137 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 GLN A 156 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 233 ASN E 264 HIS F 38 GLN F 82 HIS F 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123323 restraints weight = 37644.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126871 restraints weight = 16977.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129002 restraints weight = 10978.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130207 restraints weight = 8671.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130740 restraints weight = 7657.220| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18402 Z= 0.205 Angle : 0.889 13.490 25775 Z= 0.467 Chirality : 0.054 0.467 2882 Planarity : 0.005 0.042 2630 Dihedral : 27.750 175.982 3844 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.29 % Favored : 87.41 % Rotamer: Outliers : 6.11 % Allowed : 27.76 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.20), residues: 1700 helix: -0.58 (0.18), residues: 796 sheet: -2.39 (0.42), residues: 134 loop : -3.32 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 218 TYR 0.024 0.002 TYR D 228 PHE 0.023 0.002 PHE B 170 TRP 0.050 0.003 TRP C 268 HIS 0.024 0.001 HIS E 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (18386) covalent geometry : angle 0.88509 / 0.47 (25768) hydrogen bonds : bond 0.06840 / 4.59 ( 787) hydrogen bonds : angle 5.65989 / 3.95 ( 2045) metal coordination : bond 0.01655 / 1.20 ( 16) metal coordination : angle 5.43134 / 3.48 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 404 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8900 (pp20) cc_final: 0.8597 (pp20) REVERT: A 99 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6352 (tm-30) REVERT: A 106 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8589 (tm-30) REVERT: A 148 ASN cc_start: 0.9322 (t0) cc_final: 0.8872 (t0) REVERT: A 175 ASP cc_start: 0.8755 (p0) cc_final: 0.8406 (p0) REVERT: A 179 ASP cc_start: 0.8711 (p0) cc_final: 0.8143 (p0) REVERT: B 63 ASP cc_start: 0.8308 (t70) cc_final: 0.7913 (t0) REVERT: B 119 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6761 (t) REVERT: B 128 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: B 170 PHE cc_start: 0.8473 (p90) cc_final: 0.8070 (p90) REVERT: B 172 ASP cc_start: 0.8990 (t70) cc_final: 0.8765 (t0) REVERT: B 173 LYS cc_start: 0.8938 (ptpp) cc_final: 0.8645 (ptpp) REVERT: B 178 MET cc_start: 0.7806 (mpp) cc_final: 0.6839 (tpp) REVERT: B 179 ASP cc_start: 0.8262 (p0) cc_final: 0.7918 (p0) REVERT: B 229 TYR cc_start: 0.8774 (m-10) cc_final: 0.8214 (m-10) REVERT: B 241 LYS cc_start: 0.9333 (mppt) cc_final: 0.9086 (mppt) REVERT: C 4 GLU cc_start: 0.8414 (pp20) cc_final: 0.8090 (pp20) REVERT: C 51 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6970 (pmt-80) REVERT: C 106 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8573 (tm-30) REVERT: C 133 MET cc_start: 0.8167 (tpp) cc_final: 0.7935 (tpp) REVERT: C 148 ASN cc_start: 0.9411 (t0) cc_final: 0.8887 (t0) REVERT: C 175 ASP cc_start: 0.8646 (p0) cc_final: 0.8258 (p0) REVERT: C 178 MET cc_start: 0.7978 (tpp) cc_final: 0.7740 (tpp) REVERT: C 199 HIS cc_start: 0.8534 (m-70) cc_final: 0.8290 (m-70) REVERT: C 238 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.5883 (mmm160) REVERT: C 268 TRP cc_start: 0.8260 (m-90) cc_final: 0.7997 (m-90) REVERT: D 99 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8692 (mm-30) REVERT: D 116 TYR cc_start: 0.8576 (m-80) cc_final: 0.8290 (m-80) REVERT: D 165 LEU cc_start: 0.9370 (tp) cc_final: 0.9157 (tt) REVERT: D 200 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8870 (mmmm) REVERT: D 226 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.5901 (m-70) REVERT: E 39 GLU cc_start: 0.7623 (pm20) cc_final: 0.7382 (pm20) REVERT: E 70 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8408 (tpt170) REVERT: E 87 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5686 (mt) REVERT: E 263 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8449 (p90) REVERT: E 266 GLN cc_start: 0.8287 (pm20) cc_final: 0.8032 (pm20) REVERT: E 267 LEU cc_start: 0.9018 (pp) cc_final: 0.8275 (pp) REVERT: F 67 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: F 70 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8180 (tpp-160) REVERT: F 87 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5739 (mt) outliers start: 92 outliers final: 64 residues processed: 450 average time/residue: 0.1284 time to fit residues: 88.4045 Evaluate side-chains 466 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 392 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN F 38 GLN F 203 GLN F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.177707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121896 restraints weight = 38325.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125388 restraints weight = 17369.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127521 restraints weight = 11341.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128458 restraints weight = 9011.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129280 restraints weight = 8084.065| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18402 Z= 0.225 Angle : 0.908 14.119 25775 Z= 0.476 Chirality : 0.055 0.505 2882 Planarity : 0.005 0.044 2630 Dihedral : 27.714 176.080 3844 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.94 % Favored : 86.71 % Rotamer: Outliers : 7.30 % Allowed : 27.69 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.20), residues: 1700 helix: -0.51 (0.18), residues: 804 sheet: -2.20 (0.43), residues: 132 loop : -3.32 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 218 TYR 0.031 0.002 TYR E 209 PHE 0.042 0.002 PHE E 304 TRP 0.035 0.003 TRP A 268 HIS 0.011 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (18386) covalent geometry : angle 0.90301 / 0.48 (25768) hydrogen bonds : bond 0.06889 / 4.62 ( 787) hydrogen bonds : angle 5.68480 / 3.96 ( 2045) metal coordination : bond 0.01843 / 1.24 ( 16) metal coordination : angle 5.67790 / 3.72 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 395 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8958 (pp20) cc_final: 0.8613 (pp20) REVERT: A 99 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: A 106 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 148 ASN cc_start: 0.9330 (t0) cc_final: 0.8878 (t0) REVERT: A 175 ASP cc_start: 0.8740 (p0) cc_final: 0.8390 (p0) REVERT: A 179 ASP cc_start: 0.8739 (p0) cc_final: 0.8174 (p0) REVERT: B 63 ASP cc_start: 0.8355 (t70) cc_final: 0.7984 (t0) REVERT: B 128 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 142 THR cc_start: 0.8478 (m) cc_final: 0.8262 (p) REVERT: B 170 PHE cc_start: 0.8493 (p90) cc_final: 0.8067 (p90) REVERT: B 172 ASP cc_start: 0.9041 (t70) cc_final: 0.8748 (t0) REVERT: B 173 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8744 (ptpp) REVERT: B 178 MET cc_start: 0.7922 (mpp) cc_final: 0.6938 (tpp) REVERT: B 179 ASP cc_start: 0.8358 (p0) cc_final: 0.8075 (p0) REVERT: B 241 LYS cc_start: 0.9318 (mppt) cc_final: 0.9100 (mppt) REVERT: C 51 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6982 (pmt-80) REVERT: C 92 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6807 (ttpt) REVERT: C 133 MET cc_start: 0.8194 (tpp) cc_final: 0.7973 (tpp) REVERT: C 155 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.8966 (p) REVERT: C 175 ASP cc_start: 0.8677 (p0) cc_final: 0.8306 (p0) REVERT: C 199 HIS cc_start: 0.8556 (m-70) cc_final: 0.8303 (m-70) REVERT: C 238 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.5938 (mmm160) REVERT: C 268 TRP cc_start: 0.8339 (m-90) cc_final: 0.8118 (m-90) REVERT: D 99 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8718 (mm-30) REVERT: D 116 TYR cc_start: 0.8607 (m-80) cc_final: 0.8289 (m-80) REVERT: D 165 LEU cc_start: 0.9387 (tp) cc_final: 0.9167 (tt) REVERT: D 226 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.5750 (m-70) REVERT: D 239 GLN cc_start: 0.7730 (mp10) cc_final: 0.7386 (mp10) REVERT: E 70 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8447 (tpt170) REVERT: E 87 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5725 (mt) REVERT: E 213 TYR cc_start: 0.7517 (m-80) cc_final: 0.7127 (m-80) REVERT: E 225 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8860 (mp) REVERT: E 263 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8469 (p90) REVERT: E 266 GLN cc_start: 0.8297 (pm20) cc_final: 0.7998 (pm20) REVERT: E 267 LEU cc_start: 0.8940 (pp) cc_final: 0.8169 (pp) REVERT: E 276 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8290 (pp20) REVERT: E 293 TRP cc_start: 0.8120 (t-100) cc_final: 0.7863 (t-100) REVERT: F 67 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: F 70 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8159 (tpt170) REVERT: F 87 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5790 (mt) outliers start: 110 outliers final: 76 residues processed: 455 average time/residue: 0.1281 time to fit residues: 88.7549 Evaluate side-chains 470 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 382 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 263 TYR Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 168 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123097 restraints weight = 37628.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126581 restraints weight = 16853.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128702 restraints weight = 10912.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129903 restraints weight = 8620.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130514 restraints weight = 7628.021| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18402 Z= 0.204 Angle : 0.905 15.649 25775 Z= 0.472 Chirality : 0.054 0.468 2882 Planarity : 0.005 0.044 2630 Dihedral : 27.623 176.357 3844 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.53 % Favored : 87.12 % Rotamer: Outliers : 6.37 % Allowed : 29.22 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.20), residues: 1700 helix: -0.44 (0.18), residues: 792 sheet: -1.61 (0.49), residues: 108 loop : -3.33 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 218 TYR 0.026 0.002 TYR E 209 PHE 0.036 0.002 PHE F 304 TRP 0.040 0.002 TRP A 268 HIS 0.010 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (18386) covalent geometry : angle 0.90082 / 0.47 (25768) hydrogen bonds : bond 0.06594 / 4.42 ( 787) hydrogen bonds : angle 5.61116 / 3.91 ( 2045) metal coordination : bond 0.01661 / 1.18 ( 16) metal coordination : angle 5.14145 / 3.34 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 404 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8942 (pp20) cc_final: 0.8556 (pp20) REVERT: A 58 HIS cc_start: 0.6182 (m-70) cc_final: 0.5826 (m90) REVERT: A 106 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 148 ASN cc_start: 0.9289 (t0) cc_final: 0.8861 (t0) REVERT: A 175 ASP cc_start: 0.8695 (p0) cc_final: 0.8217 (p0) REVERT: A 179 ASP cc_start: 0.8715 (p0) cc_final: 0.8121 (p0) REVERT: B 63 ASP cc_start: 0.8332 (t70) cc_final: 0.8028 (t70) REVERT: B 128 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: B 142 THR cc_start: 0.8418 (m) cc_final: 0.8199 (p) REVERT: B 172 ASP cc_start: 0.9000 (t70) cc_final: 0.8724 (t0) REVERT: B 173 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8766 (ptpp) REVERT: B 178 MET cc_start: 0.7868 (mpp) cc_final: 0.6962 (tpp) REVERT: B 179 ASP cc_start: 0.8347 (p0) cc_final: 0.8079 (p0) REVERT: B 241 LYS cc_start: 0.9349 (mppt) cc_final: 0.9137 (mppt) REVERT: C 4 GLU cc_start: 0.8373 (pp20) cc_final: 0.8038 (pp20) REVERT: C 51 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7028 (pmt-80) REVERT: C 92 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6689 (ttpt) REVERT: C 133 MET cc_start: 0.8176 (tpp) cc_final: 0.7934 (tpp) REVERT: C 148 ASN cc_start: 0.9414 (t0) cc_final: 0.8932 (t0) REVERT: C 155 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8869 (p) REVERT: C 175 ASP cc_start: 0.8644 (p0) cc_final: 0.8280 (p0) REVERT: C 199 HIS cc_start: 0.8549 (m-70) cc_final: 0.8295 (m-70) REVERT: C 238 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.5981 (mmm160) REVERT: D 99 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8708 (mm-30) REVERT: D 116 TYR cc_start: 0.8596 (m-80) cc_final: 0.8227 (m-80) REVERT: D 165 LEU cc_start: 0.9368 (tp) cc_final: 0.9159 (tt) REVERT: D 200 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8522 (mmmm) REVERT: D 204 GLN cc_start: 0.9095 (mt0) cc_final: 0.8838 (mt0) REVERT: D 226 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.5627 (m-70) REVERT: D 239 GLN cc_start: 0.7751 (mp10) cc_final: 0.7440 (mp10) REVERT: E 70 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8432 (tpt170) REVERT: E 87 ILE cc_start: 0.6139 (OUTLIER) cc_final: 0.5662 (mt) REVERT: E 225 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8880 (mp) REVERT: E 263 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8509 (p90) REVERT: E 266 GLN cc_start: 0.8346 (pm20) cc_final: 0.8044 (pm20) REVERT: E 267 LEU cc_start: 0.8969 (pp) cc_final: 0.8230 (pp) REVERT: E 276 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8280 (pp20) REVERT: E 293 TRP cc_start: 0.8014 (t-100) cc_final: 0.7670 (t-100) REVERT: F 70 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8170 (tpt170) REVERT: F 87 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5699 (mt) outliers start: 96 outliers final: 74 residues processed: 453 average time/residue: 0.1299 time to fit residues: 90.2634 Evaluate side-chains 469 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 385 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 268 TRP Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 263 TYR Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 49 optimal weight: 6.9990 chunk 128 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 34 optimal weight: 0.0980 chunk 111 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.182113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127199 restraints weight = 38061.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130893 restraints weight = 17163.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133090 restraints weight = 11108.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134335 restraints weight = 8789.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134857 restraints weight = 7778.557| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18402 Z= 0.171 Angle : 0.902 15.770 25775 Z= 0.468 Chirality : 0.054 0.473 2882 Planarity : 0.005 0.043 2630 Dihedral : 27.475 176.033 3844 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.47 % Favored : 88.18 % Rotamer: Outliers : 5.25 % Allowed : 30.41 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.20), residues: 1700 helix: -0.43 (0.18), residues: 790 sheet: -1.47 (0.47), residues: 104 loop : -3.29 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 218 TYR 0.021 0.002 TYR D 228 PHE 0.029 0.002 PHE B 170 TRP 0.051 0.002 TRP A 268 HIS 0.008 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (18386) covalent geometry : angle 0.90026 / 0.47 (25768) hydrogen bonds : bond 0.06170 / 4.12 ( 787) hydrogen bonds : angle 5.46933 / 3.80 ( 2045) metal coordination : bond 0.01697 / 1.27 ( 16) metal coordination : angle 3.75259 / 2.36 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 419 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8852 (pp20) cc_final: 0.8467 (pp20) REVERT: A 99 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: A 106 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 175 ASP cc_start: 0.8612 (p0) cc_final: 0.8135 (p0) REVERT: A 179 ASP cc_start: 0.8651 (p0) cc_final: 0.8130 (p0) REVERT: B 63 ASP cc_start: 0.8502 (t70) cc_final: 0.8149 (t70) REVERT: B 67 PHE cc_start: 0.7888 (t80) cc_final: 0.7661 (t80) REVERT: B 128 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8413 (tm-30) REVERT: B 173 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8755 (ptpp) REVERT: B 178 MET cc_start: 0.7816 (mpp) cc_final: 0.6987 (tpp) REVERT: B 179 ASP cc_start: 0.8282 (p0) cc_final: 0.7944 (p0) REVERT: B 241 LYS cc_start: 0.9363 (mppt) cc_final: 0.8907 (mtmm) REVERT: C 4 GLU cc_start: 0.8324 (pp20) cc_final: 0.7911 (pp20) REVERT: C 51 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6964 (pmt-80) REVERT: C 106 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 133 MET cc_start: 0.8116 (tpp) cc_final: 0.7881 (tpp) REVERT: C 155 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8722 (p) REVERT: C 175 ASP cc_start: 0.8603 (p0) cc_final: 0.8225 (p0) REVERT: C 199 HIS cc_start: 0.8516 (m-70) cc_final: 0.8282 (m-70) REVERT: C 238 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6072 (mmm160) REVERT: D 99 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8674 (mm-30) REVERT: D 116 TYR cc_start: 0.8551 (m-80) cc_final: 0.8187 (m-80) REVERT: D 165 LEU cc_start: 0.9342 (tp) cc_final: 0.9132 (tt) REVERT: D 226 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.5385 (m-70) REVERT: E 67 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: E 70 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8442 (tpt170) REVERT: E 81 THR cc_start: 0.7751 (m) cc_final: 0.7320 (p) REVERT: E 87 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5640 (mt) REVERT: E 208 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.9017 (m-10) REVERT: E 225 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8853 (mp) REVERT: E 263 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8496 (p90) REVERT: E 266 GLN cc_start: 0.8368 (pm20) cc_final: 0.8077 (pm20) REVERT: E 267 LEU cc_start: 0.8942 (pp) cc_final: 0.8214 (pp) REVERT: E 276 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8299 (pp20) REVERT: E 293 TRP cc_start: 0.8054 (t-100) cc_final: 0.7610 (t-100) REVERT: F 70 ARG cc_start: 0.8611 (tpp-160) cc_final: 0.8247 (tpp-160) REVERT: F 87 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5671 (mt) REVERT: F 213 TYR cc_start: 0.7859 (m-80) cc_final: 0.7616 (m-80) outliers start: 79 outliers final: 53 residues processed: 457 average time/residue: 0.1285 time to fit residues: 89.8610 Evaluate side-chains 453 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 388 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 40.0000 chunk 171 optimal weight: 20.0000 chunk 7 optimal weight: 0.3980 chunk 154 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 150 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 2.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS F 203 GLN F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.180425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126775 restraints weight = 37546.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130313 restraints weight = 16744.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132435 restraints weight = 10747.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133640 restraints weight = 8452.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134166 restraints weight = 7456.830| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18402 Z= 0.199 Angle : 0.917 14.350 25775 Z= 0.477 Chirality : 0.054 0.499 2882 Planarity : 0.005 0.043 2630 Dihedral : 27.458 174.935 3844 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.82 % Favored : 86.82 % Rotamer: Outliers : 5.11 % Allowed : 31.21 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.20), residues: 1700 helix: -0.39 (0.18), residues: 790 sheet: -1.58 (0.48), residues: 108 loop : -3.26 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 218 TYR 0.026 0.002 TYR F 213 PHE 0.027 0.002 PHE F 99 TRP 0.055 0.002 TRP A 268 HIS 0.009 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (18386) covalent geometry : angle 0.91412 / 0.48 (25768) hydrogen bonds : bond 0.06378 / 4.25 ( 787) hydrogen bonds : angle 5.53543 / 3.86 ( 2045) metal coordination : bond 0.01463 / 1.05 ( 16) metal coordination : angle 4.32789 / 2.80 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 388 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8894 (pp20) cc_final: 0.8482 (pp20) REVERT: A 99 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6279 (tm-30) REVERT: A 106 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 175 ASP cc_start: 0.8631 (p0) cc_final: 0.8164 (p0) REVERT: A 179 ASP cc_start: 0.8699 (p0) cc_final: 0.8152 (p0) REVERT: B 63 ASP cc_start: 0.8496 (t70) cc_final: 0.8187 (t70) REVERT: B 128 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8430 (tm-30) REVERT: B 178 MET cc_start: 0.7831 (mpp) cc_final: 0.6903 (tpp) REVERT: B 179 ASP cc_start: 0.8343 (p0) cc_final: 0.8029 (p0) REVERT: C 4 GLU cc_start: 0.8330 (pp20) cc_final: 0.7903 (pp20) REVERT: C 51 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6919 (pmt-80) REVERT: C 92 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6586 (ttpt) REVERT: C 133 MET cc_start: 0.8130 (tpp) cc_final: 0.7908 (tpp) REVERT: C 155 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8823 (p) REVERT: C 175 ASP cc_start: 0.8596 (p0) cc_final: 0.8225 (p0) REVERT: C 199 HIS cc_start: 0.8543 (m-70) cc_final: 0.8298 (m-70) REVERT: C 238 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6060 (mmm160) REVERT: D 99 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8677 (mm-30) REVERT: D 116 TYR cc_start: 0.8587 (m-80) cc_final: 0.8231 (m-80) REVERT: D 165 LEU cc_start: 0.9374 (tp) cc_final: 0.9134 (tt) REVERT: D 226 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.5386 (m-70) REVERT: D 239 GLN cc_start: 0.7776 (mp10) cc_final: 0.7476 (mp10) REVERT: E 70 ARG cc_start: 0.8841 (ttm-80) cc_final: 0.8438 (tpt170) REVERT: E 87 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5561 (mt) REVERT: E 225 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8830 (mp) REVERT: E 263 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8529 (p90) REVERT: E 266 GLN cc_start: 0.8394 (pm20) cc_final: 0.8095 (pm20) REVERT: E 267 LEU cc_start: 0.8952 (pp) cc_final: 0.8246 (pp) REVERT: E 276 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8300 (pp20) REVERT: E 293 TRP cc_start: 0.8052 (t-100) cc_final: 0.7596 (t-100) REVERT: F 70 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8174 (tpt170) REVERT: F 87 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5641 (mt) outliers start: 77 outliers final: 58 residues processed: 430 average time/residue: 0.1236 time to fit residues: 81.6873 Evaluate side-chains 447 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 378 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 5.9990 chunk 94 optimal weight: 0.0170 chunk 81 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 143 optimal weight: 0.0170 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 52 optimal weight: 8.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS E 203 GLN E 233 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS F 203 GLN F 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.185328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131942 restraints weight = 38050.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135695 restraints weight = 16875.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137963 restraints weight = 10769.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139267 restraints weight = 8435.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139814 restraints weight = 7418.607| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18402 Z= 0.174 Angle : 0.935 15.466 25775 Z= 0.480 Chirality : 0.054 0.388 2882 Planarity : 0.005 0.051 2630 Dihedral : 27.292 175.355 3844 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.59 % Favored : 89.12 % Rotamer: Outliers : 4.52 % Allowed : 31.94 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1700 helix: -0.30 (0.18), residues: 772 sheet: -1.49 (0.46), residues: 104 loop : -3.13 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 218 TYR 0.026 0.002 TYR E 209 PHE 0.029 0.002 PHE E 99 TRP 0.069 0.002 TRP A 268 HIS 0.007 0.001 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (18386) covalent geometry : angle 0.93316 / 0.48 (25768) hydrogen bonds : bond 0.05816 / 3.88 ( 787) hydrogen bonds : angle 5.43318 / 3.76 ( 2045) metal coordination : bond 0.01875 / 1.38 ( 16) metal coordination : angle 3.46328 / 2.30 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.98 seconds wall clock time: 75 minutes 32.46 seconds (4532.46 seconds total)