Starting phenix.real_space_refine on Wed Mar 4 23:32:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6voy_21301/03_2026/6voy_21301.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voy_21301/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6voy_21301/03_2026/6voy_21301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voy_21301/03_2026/6voy_21301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6voy_21301/03_2026/6voy_21301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voy_21301/03_2026/6voy_21301.map" } 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-dev-5986/lib/python3.9/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: 3.93, per 1000 atoms: 0.22 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: 1.64 Conformation dependent library (CDL) restraints added in 664.2 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: 2.16 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: 2.94 Time building geometry restraints manager: 2.11 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=" CG PRO D 243 " pdb=" CD PRO D 243 " ideal model delta sigma weight residual 1.503 1.348 0.155 3.40e-02 8.65e+02 2.09e+01 bond pdb=" CB TRP A 240 " pdb=" CG TRP A 240 " ideal model delta sigma weight residual 1.498 1.362 0.136 3.10e-02 1.04e+03 1.94e+01 bond pdb=" CB TRP C 60 " pdb=" CG TRP C 60 " ideal model delta sigma weight residual 1.498 1.368 0.130 3.10e-02 1.04e+03 1.76e+01 bond pdb=" CB ASN B 118 " pdb=" CG ASN B 118 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.52e+01 bond pdb=" CB TRP C 240 " pdb=" CG TRP C 240 " ideal model delta sigma weight residual 1.498 1.388 0.110 3.10e-02 1.04e+03 1.25e+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=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " ideal model delta sigma weight residual 110.63 83.38 27.25 1.94e+00 2.66e-01 1.97e+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: 0.00 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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= 0.592 Angle : 1.578 43.689 25775 Z= 0.891 Chirality : 0.100 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 covalent geometry : bond 0.01259 (18386) covalent geometry : angle 1.52161 (25768) hydrogen bonds : bond 0.15093 ( 787) hydrogen bonds : angle 8.18449 ( 2045) metal coordination : bond 0.13404 ( 16) metal coordination : angle 25.50425 ( 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 : 0.540 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: 0.8451 (p0) REVERT: A 179 ASP cc_start: 0.8924 (p0) cc_final: 0.8463 (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: 0.8846 (m-30) REVERT: B 241 LYS cc_start: 0.9315 (mppt) cc_final: 0.8819 (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: 0.9068 (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: 0.9216 (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: 0.8906 (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: 0.1378 time to fit residues: 89.0528 Evaluate side-chains 371 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS D 61 GLN D 77 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 133 HIS E 187 HIS E 205 ASN E 233 ASN E 306 ASN F 48 GLN F 85 ASN F 187 HIS F 205 ASN F 233 ASN F 306 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.178626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121876 restraints weight = 38055.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125346 restraints weight = 17433.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127468 restraints weight = 11398.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128667 restraints weight = 9060.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129211 restraints weight = 8007.996| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 18402 Z= 0.271 Angle : 0.975 18.276 25775 Z= 0.518 Chirality : 0.053 0.426 2882 Planarity : 0.007 0.068 2630 Dihedral : 28.356 176.517 3850 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.59 % Allowed : 14.00 % Favored : 85.41 % Rotamer: Outliers : 3.52 % Allowed : 21.18 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.81 % 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: -4.16 (0.18), residues: 1700 helix: -1.89 (0.16), residues: 758 sheet: -2.59 (0.45), residues: 108 loop : -3.73 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 201 TYR 0.034 0.002 TYR E 209 PHE 0.022 0.002 PHE B 170 TRP 0.028 0.003 TRP F 131 HIS 0.014 0.002 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00593 (18386) covalent geometry : angle 0.96338 (25768) hydrogen bonds : bond 0.08595 ( 787) hydrogen bonds : angle 6.46823 ( 2045) metal coordination : bond 0.03025 ( 16) metal coordination : angle 9.18501 ( 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 481 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 428 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 175 ASP cc_start: 0.8857 (p0) cc_final: 0.8373 (p0) REVERT: A 179 ASP cc_start: 0.8865 (p0) cc_final: 0.8332 (p0) REVERT: A 184 ILE cc_start: 0.9443 (mm) cc_final: 0.9241 (mt) REVERT: A 245 GLU cc_start: 0.8499 (pm20) cc_final: 0.8298 (pm20) REVERT: B 139 ILE cc_start: 0.9407 (mm) cc_final: 0.9157 (mm) REVERT: B 229 TYR cc_start: 0.8714 (m-10) cc_final: 0.8165 (m-10) REVERT: B 241 LYS cc_start: 0.9305 (mppt) cc_final: 0.9070 (mppt) REVERT: C 13 GLN cc_start: 0.8877 (pm20) cc_final: 0.8166 (pp30) REVERT: C 106 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 133 MET cc_start: 0.8190 (tpp) cc_final: 0.7974 (tpp) REVERT: C 175 ASP cc_start: 0.8776 (p0) cc_final: 0.8410 (p0) REVERT: C 186 LEU cc_start: 0.9392 (tt) cc_final: 0.9178 (tp) REVERT: D 99 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8742 (mm-30) REVERT: D 116 TYR cc_start: 0.8546 (m-80) cc_final: 0.8252 (m-80) REVERT: E 70 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8335 (tpp-160) REVERT: E 103 MET cc_start: 0.8625 (pmm) cc_final: 0.8348 (pmm) REVERT: E 141 PHE cc_start: 0.9266 (t80) cc_final: 0.8998 (t80) REVERT: E 178 GLU cc_start: 0.9247 (pp20) cc_final: 0.9032 (pp20) REVERT: E 203 GLN cc_start: 0.9499 (tp-100) cc_final: 0.9160 (mm-40) REVERT: E 307 GLU cc_start: 0.9095 (tp30) cc_final: 0.8753 (tp30) REVERT: F 70 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8341 (tpp80) REVERT: F 103 MET cc_start: 0.8639 (pmm) cc_final: 0.8432 (pmm) REVERT: F 178 GLU cc_start: 0.9217 (pp20) cc_final: 0.8983 (pp20) REVERT: F 203 GLN cc_start: 0.9503 (tp-100) cc_final: 0.9155 (mm-40) REVERT: F 307 GLU cc_start: 0.9158 (tp30) cc_final: 0.8800 (tp30) outliers start: 53 outliers final: 40 residues processed: 449 average time/residue: 0.1347 time to fit residues: 92.1647 Evaluate side-chains 428 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 388 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 108 ILE 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 159 ASN 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 80 VAL 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 214 ILE 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 81 THR Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 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 260 LEU 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 49 CYS Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 189 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 96 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 160 optimal weight: 0.0670 chunk 112 optimal weight: 5.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 132 ASN 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 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 148 ASN D 191 HIS ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 206 ASN E 243 HIS F 38 GLN F 82 HIS F 206 ASN F 233 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 = 0.4327 r_free = 0.4327 target = 0.183122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128231 restraints weight = 37770.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131879 restraints weight = 17320.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134123 restraints weight = 11289.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135382 restraints weight = 8892.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136073 restraints weight = 7833.654| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18402 Z= 0.199 Angle : 0.869 17.546 25775 Z= 0.461 Chirality : 0.049 0.386 2882 Planarity : 0.005 0.043 2630 Dihedral : 27.988 177.729 3844 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.59 % Favored : 89.06 % Rotamer: Outliers : 5.31 % Allowed : 22.44 % Favored : 72.24 % 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: -3.35 (0.19), residues: 1700 helix: -0.91 (0.18), residues: 774 sheet: -2.89 (0.38), residues: 150 loop : -3.56 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 157 TYR 0.031 0.002 TYR E 209 PHE 0.022 0.002 PHE B 170 TRP 0.045 0.002 TRP A 268 HIS 0.011 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00406 (18386) covalent geometry : angle 0.86071 (25768) hydrogen bonds : bond 0.06881 ( 787) hydrogen bonds : angle 5.77196 ( 2045) metal coordination : bond 0.02239 ( 16) metal coordination : angle 7.45240 ( 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 523 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 443 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8924 (pp20) cc_final: 0.8590 (pp20) REVERT: A 13 GLN cc_start: 0.8628 (pm20) cc_final: 0.8354 (pp30) REVERT: A 106 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8503 (tm-30) REVERT: A 175 ASP cc_start: 0.8764 (p0) cc_final: 0.8386 (p0) REVERT: A 179 ASP cc_start: 0.8599 (p0) cc_final: 0.8143 (p0) REVERT: B 128 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: B 170 PHE cc_start: 0.8665 (p90) cc_final: 0.8334 (p90) REVERT: B 175 ASP cc_start: 0.8552 (t0) cc_final: 0.8322 (t0) REVERT: B 178 MET cc_start: 0.7895 (mpp) cc_final: 0.7107 (tpp) REVERT: B 227 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: B 229 TYR cc_start: 0.8691 (m-10) cc_final: 0.8158 (m-10) REVERT: B 245 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7479 (mm-30) REVERT: C 13 GLN cc_start: 0.8840 (pm20) cc_final: 0.8445 (pp30) REVERT: C 63 ASP cc_start: 0.8038 (t0) cc_final: 0.7733 (t0) REVERT: C 106 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8462 (tm-30) REVERT: C 133 MET cc_start: 0.8177 (tpp) cc_final: 0.7951 (tpp) REVERT: C 172 ASP cc_start: 0.8341 (t0) cc_final: 0.8024 (t0) REVERT: C 175 ASP cc_start: 0.8712 (p0) cc_final: 0.8346 (p0) REVERT: C 199 HIS cc_start: 0.8621 (m-70) cc_final: 0.8339 (m-70) REVERT: C 228 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8025 (p90) REVERT: C 249 GLU cc_start: 0.8621 (tp30) cc_final: 0.8383 (tp30) REVERT: D 99 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8752 (mm-30) REVERT: D 116 TYR cc_start: 0.8570 (m-80) cc_final: 0.8333 (m-80) REVERT: D 204 GLN cc_start: 0.8977 (mt0) cc_final: 0.8739 (mt0) REVERT: E 70 ARG cc_start: 0.8826 (ttm-80) cc_final: 0.8384 (tpp-160) REVERT: E 87 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5916 (mt) REVERT: E 141 PHE cc_start: 0.9286 (t80) cc_final: 0.8891 (t80) REVERT: E 178 GLU cc_start: 0.9230 (pp20) cc_final: 0.8936 (pp20) REVERT: E 203 GLN cc_start: 0.9462 (tp-100) cc_final: 0.9070 (mm-40) REVERT: E 263 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8336 (p90) REVERT: E 266 GLN cc_start: 0.8099 (pm20) cc_final: 0.7742 (pm20) REVERT: E 267 LEU cc_start: 0.8971 (pp) cc_final: 0.8195 (pp) REVERT: E 320 PHE cc_start: 0.6702 (t80) cc_final: 0.6461 (t80) REVERT: F 70 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8280 (tpp80) REVERT: F 87 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.5968 (mt) REVERT: F 178 GLU cc_start: 0.9233 (pp20) cc_final: 0.8890 (pp20) REVERT: F 203 GLN cc_start: 0.9471 (tp-100) cc_final: 0.9074 (mm-40) REVERT: F 213 TYR cc_start: 0.7728 (m-80) cc_final: 0.7430 (m-80) outliers start: 80 outliers final: 46 residues processed: 481 average time/residue: 0.1355 time to fit residues: 98.0027 Evaluate side-chains 452 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 400 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 145 VAL 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 214 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS 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 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 308 LEU 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 169 GLU 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 275 LEU Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.0020 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 100 optimal weight: 0.0370 chunk 32 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 0.0010 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 204 GLN ** 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 156 GLN E 264 HIS F 38 GLN F 233 ASN F 243 HIS F 264 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.183178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129392 restraints weight = 38494.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133235 restraints weight = 17171.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135581 restraints weight = 10985.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136908 restraints weight = 8590.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137492 restraints weight = 7530.692| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18402 Z= 0.175 Angle : 0.829 13.687 25775 Z= 0.436 Chirality : 0.047 0.348 2882 Planarity : 0.005 0.043 2630 Dihedral : 27.635 177.959 3844 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.47 % Favored : 88.29 % Rotamer: Outliers : 5.64 % Allowed : 23.44 % Favored : 70.92 % 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: -2.78 (0.20), residues: 1700 helix: -0.41 (0.18), residues: 776 sheet: -2.33 (0.43), residues: 134 loop : -3.35 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 269 TYR 0.029 0.002 TYR D 228 PHE 0.020 0.002 PHE B 170 TRP 0.047 0.002 TRP A 268 HIS 0.008 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00370 (18386) covalent geometry : angle 0.82424 (25768) hydrogen bonds : bond 0.05968 ( 787) hydrogen bonds : angle 5.41433 ( 2045) metal coordination : bond 0.02141 ( 16) metal coordination : angle 5.25075 ( 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 545 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 460 time to evaluate : 0.571 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: A 4 GLU cc_start: 0.8897 (pp20) cc_final: 0.8546 (pp20) REVERT: A 13 GLN cc_start: 0.8782 (pm20) cc_final: 0.8531 (pp30) REVERT: A 106 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8529 (tm-30) REVERT: A 148 ASN cc_start: 0.9331 (t0) cc_final: 0.8872 (t0) REVERT: A 175 ASP cc_start: 0.8708 (p0) cc_final: 0.8242 (p0) REVERT: A 179 ASP cc_start: 0.8631 (p0) cc_final: 0.8277 (p0) REVERT: B 63 ASP cc_start: 0.8354 (t70) cc_final: 0.8061 (t70) REVERT: B 119 THR cc_start: 0.6559 (OUTLIER) cc_final: 0.6280 (t) REVERT: B 128 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: B 170 PHE cc_start: 0.8433 (p90) cc_final: 0.8093 (p90) REVERT: B 178 MET cc_start: 0.7784 (mpp) cc_final: 0.6952 (tpp) REVERT: B 179 ASP cc_start: 0.8325 (p0) cc_final: 0.7995 (p0) REVERT: B 227 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: B 245 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7527 (mm-30) REVERT: C 13 GLN cc_start: 0.8888 (pm20) cc_final: 0.8638 (pp30) REVERT: C 106 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 133 MET cc_start: 0.8212 (tpp) cc_final: 0.7962 (tpp) REVERT: C 148 ASN cc_start: 0.9433 (t0) cc_final: 0.8903 (t0) REVERT: C 175 ASP cc_start: 0.8635 (p0) cc_final: 0.8256 (p0) REVERT: C 228 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7518 (p90) REVERT: D 99 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8694 (mm-30) REVERT: D 116 TYR cc_start: 0.8584 (m-80) cc_final: 0.8271 (m-80) REVERT: D 204 GLN cc_start: 0.8914 (mt0) cc_final: 0.8677 (mt0) REVERT: E 70 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8404 (tpp-160) REVERT: E 76 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8931 (ptp) REVERT: E 81 THR cc_start: 0.7702 (m) cc_final: 0.7247 (p) REVERT: E 87 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5826 (mt) REVERT: E 136 LEU cc_start: 0.9309 (mt) cc_final: 0.9104 (mt) REVERT: E 183 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9247 (ttpt) REVERT: E 213 TYR cc_start: 0.7830 (m-80) cc_final: 0.7514 (m-80) REVERT: E 263 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8510 (p90) REVERT: E 266 GLN cc_start: 0.8139 (pm20) cc_final: 0.7755 (pm20) REVERT: E 267 LEU cc_start: 0.8913 (pp) cc_final: 0.8224 (pp) REVERT: E 276 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8303 (pp20) REVERT: E 293 TRP cc_start: 0.8246 (t-100) cc_final: 0.6885 (t-100) REVERT: E 311 ILE cc_start: 0.9285 (mm) cc_final: 0.9066 (mm) REVERT: F 70 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8402 (tpp-160) REVERT: F 81 THR cc_start: 0.7646 (m) cc_final: 0.7188 (p) REVERT: F 87 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5829 (mt) REVERT: F 175 ASP cc_start: 0.7915 (t0) cc_final: 0.7389 (t0) REVERT: F 226 GLU cc_start: 0.9177 (mp0) cc_final: 0.8857 (mp0) outliers start: 85 outliers final: 46 residues processed: 498 average time/residue: 0.1366 time to fit residues: 102.3771 Evaluate side-chains 473 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL 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 119 THR Chi-restraints excluded: chain B residue 128 GLN 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 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 82 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 228 TYR 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 E residue 49 CYS Chi-restraints excluded: chain E residue 76 MET 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 243 HIS 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 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 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 306 ASN 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: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 233 ASN E 264 HIS F 38 GLN F 82 HIS F 187 HIS F 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.176722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122176 restraints weight = 38013.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125602 restraints weight = 17367.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127693 restraints weight = 11321.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128850 restraints weight = 8980.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129451 restraints weight = 7956.178| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18402 Z= 0.279 Angle : 0.896 14.022 25775 Z= 0.470 Chirality : 0.049 0.383 2882 Planarity : 0.005 0.042 2630 Dihedral : 27.651 178.846 3844 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.12 % Favored : 86.65 % Rotamer: Outliers : 6.71 % Allowed : 25.83 % Favored : 67.46 % 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: -2.75 (0.20), residues: 1700 helix: -0.49 (0.18), residues: 794 sheet: -1.68 (0.48), residues: 110 loop : -3.36 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 218 TYR 0.027 0.002 TYR F 209 PHE 0.029 0.002 PHE F 304 TRP 0.048 0.003 TRP A 268 HIS 0.021 0.002 HIS E 264 Details of bonding type rmsd covalent geometry : bond 0.00626 (18386) covalent geometry : angle 0.89128 (25768) hydrogen bonds : bond 0.06726 ( 787) hydrogen bonds : angle 5.66146 ( 2045) metal coordination : bond 0.01791 ( 16) metal coordination : angle 5.82168 ( 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 512 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 411 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8984 (pp20) cc_final: 0.8586 (pp20) REVERT: A 13 GLN cc_start: 0.8837 (pm20) cc_final: 0.8480 (pp30) REVERT: A 106 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 148 ASN cc_start: 0.9339 (t0) cc_final: 0.8873 (t0) REVERT: A 175 ASP cc_start: 0.8681 (p0) cc_final: 0.8190 (p0) REVERT: A 179 ASP cc_start: 0.8707 (p0) cc_final: 0.8171 (p0) REVERT: A 273 ARG cc_start: 0.7211 (ttt90) cc_final: 0.6588 (ttt-90) REVERT: B 63 ASP cc_start: 0.8465 (t70) cc_final: 0.8194 (t70) REVERT: B 64 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8741 (mt) REVERT: B 119 THR cc_start: 0.7132 (OUTLIER) cc_final: 0.6794 (t) REVERT: B 128 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: B 170 PHE cc_start: 0.8680 (p90) cc_final: 0.8382 (p90) REVERT: B 178 MET cc_start: 0.7905 (mpp) cc_final: 0.6984 (tpp) REVERT: B 179 ASP cc_start: 0.8371 (p0) cc_final: 0.8165 (p0) REVERT: B 245 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8082 (mm-30) REVERT: C 13 GLN cc_start: 0.8883 (pm20) cc_final: 0.8557 (pp30) REVERT: C 51 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6929 (pmt-80) REVERT: C 106 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 133 MET cc_start: 0.8179 (tpp) cc_final: 0.7968 (tpp) REVERT: C 148 ASN cc_start: 0.9450 (t0) cc_final: 0.8905 (t0) REVERT: C 155 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8954 (p) REVERT: C 175 ASP cc_start: 0.8664 (p0) cc_final: 0.8323 (p0) REVERT: C 179 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8090 (p0) REVERT: C 228 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7513 (p90) REVERT: C 230 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5875 (p90) REVERT: C 249 GLU cc_start: 0.8634 (tp30) cc_final: 0.8088 (tp30) REVERT: D 99 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8733 (mm-30) REVERT: D 241 LYS cc_start: 0.9291 (mmtp) cc_final: 0.9078 (mmtm) REVERT: E 70 ARG cc_start: 0.8824 (ttm-80) cc_final: 0.8440 (tpp-160) REVERT: E 76 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8922 (ptp) REVERT: E 87 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5871 (mt) REVERT: E 136 LEU cc_start: 0.9343 (mt) cc_final: 0.9025 (mt) REVERT: E 178 GLU cc_start: 0.9067 (pp20) cc_final: 0.8846 (pp20) REVERT: E 276 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8369 (pp20) REVERT: E 293 TRP cc_start: 0.8116 (t-100) cc_final: 0.7795 (t-100) REVERT: F 70 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8318 (tpp-160) REVERT: F 87 ILE cc_start: 0.6296 (OUTLIER) cc_final: 0.5906 (mt) REVERT: F 276 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8439 (pp20) outliers start: 101 outliers final: 67 residues processed: 466 average time/residue: 0.1302 time to fit residues: 92.3155 Evaluate side-chains 461 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 383 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 THR 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 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 ILE 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 186 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 247 LEU 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 78 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP 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 228 TYR Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 78 VAL 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 76 MET 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 219 ASN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS 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 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 226 GLU 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 275 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 137 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.179453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124284 restraints weight = 37765.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128050 restraints weight = 16406.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130333 restraints weight = 10423.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131618 restraints weight = 8146.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132320 restraints weight = 7166.970| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18402 Z= 0.202 Angle : 0.879 13.887 25775 Z= 0.453 Chirality : 0.049 0.416 2882 Planarity : 0.005 0.041 2630 Dihedral : 27.515 178.002 3844 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.94 % Favored : 87.82 % Rotamer: Outliers : 6.11 % Allowed : 27.56 % Favored : 66.33 % 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: -2.62 (0.20), residues: 1700 helix: -0.33 (0.18), residues: 796 sheet: -1.64 (0.48), residues: 110 loop : -3.36 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 218 TYR 0.024 0.002 TYR E 209 PHE 0.025 0.002 PHE F 304 TRP 0.038 0.002 TRP A 268 HIS 0.009 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00448 (18386) covalent geometry : angle 0.87558 (25768) hydrogen bonds : bond 0.06143 ( 787) hydrogen bonds : angle 5.53097 ( 2045) metal coordination : bond 0.01536 ( 16) metal coordination : angle 4.55521 ( 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 494 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 402 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.9011 (pp20) cc_final: 0.8545 (pp20) REVERT: A 13 GLN cc_start: 0.8878 (pm20) cc_final: 0.8500 (pp30) REVERT: A 106 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8641 (tm-30) REVERT: A 148 ASN cc_start: 0.9331 (t0) cc_final: 0.8900 (t0) REVERT: A 175 ASP cc_start: 0.8699 (p0) cc_final: 0.8235 (p0) REVERT: A 179 ASP cc_start: 0.8733 (p0) cc_final: 0.8218 (p0) REVERT: B 63 ASP cc_start: 0.8484 (t70) cc_final: 0.8121 (t70) REVERT: B 64 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 119 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6795 (t) REVERT: B 128 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: B 170 PHE cc_start: 0.8604 (p90) cc_final: 0.8273 (p90) REVERT: B 178 MET cc_start: 0.7924 (mpp) cc_final: 0.6862 (tpp) REVERT: B 179 ASP cc_start: 0.8343 (p0) cc_final: 0.8052 (p0) REVERT: B 227 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.7768 (m100) REVERT: C 13 GLN cc_start: 0.8880 (pm20) cc_final: 0.8664 (pp30) REVERT: C 106 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 133 MET cc_start: 0.8253 (tpp) cc_final: 0.8014 (tpp) REVERT: C 148 ASN cc_start: 0.9479 (t0) cc_final: 0.8976 (t0) REVERT: C 155 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8786 (p) REVERT: C 175 ASP cc_start: 0.8693 (p0) cc_final: 0.8349 (p0) REVERT: C 228 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7567 (p90) REVERT: C 230 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.6225 (p90) REVERT: D 99 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8756 (mm-30) REVERT: D 204 GLN cc_start: 0.9076 (mt0) cc_final: 0.8861 (mt0) REVERT: E 70 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8462 (tpp-160) REVERT: E 81 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7259 (p) REVERT: E 87 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5827 (mt) REVERT: E 136 LEU cc_start: 0.9355 (mt) cc_final: 0.9109 (mt) REVERT: E 183 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9207 (ttmt) REVERT: E 263 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8656 (p90) REVERT: E 276 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8386 (pp20) REVERT: E 293 TRP cc_start: 0.8059 (t-100) cc_final: 0.7404 (t-100) REVERT: E 304 PHE cc_start: 0.8688 (t80) cc_final: 0.8486 (t80) REVERT: F 70 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8295 (tpp-160) REVERT: F 87 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5788 (mt) REVERT: F 178 GLU cc_start: 0.9046 (pp20) cc_final: 0.8830 (pp20) REVERT: F 241 GLU cc_start: 0.9054 (mp0) cc_final: 0.8828 (mm-30) REVERT: F 276 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8472 (pp20) outliers start: 92 outliers final: 61 residues processed: 455 average time/residue: 0.1349 time to fit residues: 93.8339 Evaluate side-chains 461 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 389 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 THR 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 230 PHE 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 101 ILE 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 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 B residue 258 VAL 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 117 ILE 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 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 230 PHE 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 221 SER Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 247 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 219 ASN 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 285 VAL 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 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 226 GLU 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 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: 0.8980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 46 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 66 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.180693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126190 restraints weight = 38003.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129886 restraints weight = 16946.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132144 restraints weight = 10848.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133413 restraints weight = 8497.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133984 restraints weight = 7473.222| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18402 Z= 0.179 Angle : 0.867 12.868 25775 Z= 0.445 Chirality : 0.049 0.422 2882 Planarity : 0.005 0.043 2630 Dihedral : 27.356 177.553 3844 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.88 % Favored : 87.88 % Rotamer: Outliers : 5.31 % Allowed : 28.02 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.46 (0.20), residues: 1700 helix: -0.25 (0.18), residues: 794 sheet: -0.95 (0.51), residues: 84 loop : -3.27 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 218 TYR 0.030 0.002 TYR D 228 PHE 0.021 0.002 PHE F 163 TRP 0.045 0.002 TRP A 268 HIS 0.008 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00392 (18386) covalent geometry : angle 0.86528 (25768) hydrogen bonds : bond 0.05764 ( 787) hydrogen bonds : angle 5.39367 ( 2045) metal coordination : bond 0.01371 ( 16) metal coordination : angle 3.52417 ( 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 498 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 418 time to evaluate : 0.571 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: A 13 GLN cc_start: 0.8882 (pm20) cc_final: 0.8535 (pp30) REVERT: A 106 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 175 ASP cc_start: 0.8585 (p0) cc_final: 0.8121 (p0) REVERT: A 179 ASP cc_start: 0.8689 (p0) cc_final: 0.8193 (p0) REVERT: B 63 ASP cc_start: 0.8400 (t70) cc_final: 0.8014 (t70) REVERT: B 64 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 119 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6738 (t) REVERT: B 128 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: B 170 PHE cc_start: 0.8452 (p90) cc_final: 0.8095 (p90) REVERT: B 178 MET cc_start: 0.7852 (mpp) cc_final: 0.6877 (tpp) REVERT: B 179 ASP cc_start: 0.8279 (p0) cc_final: 0.7930 (p0) REVERT: B 227 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: B 245 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 13 GLN cc_start: 0.8792 (pm20) cc_final: 0.8585 (pp30) REVERT: C 51 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6865 (pmt-80) REVERT: C 106 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 133 MET cc_start: 0.8212 (tpp) cc_final: 0.7982 (tpp) REVERT: C 155 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 175 ASP cc_start: 0.8594 (p0) cc_final: 0.8235 (p0) REVERT: C 179 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7991 (p0) REVERT: C 228 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7389 (p90) REVERT: C 230 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5898 (p90) REVERT: D 99 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8725 (mm-30) REVERT: E 70 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8351 (tpp-160) REVERT: E 81 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7332 (p) REVERT: E 87 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5707 (mt) REVERT: E 136 LEU cc_start: 0.9338 (mt) cc_final: 0.9078 (mt) REVERT: E 166 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8453 (mm110) REVERT: E 183 LYS cc_start: 0.9503 (ttpt) cc_final: 0.9217 (ttpt) REVERT: E 276 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8535 (pp20) REVERT: E 293 TRP cc_start: 0.8044 (t-100) cc_final: 0.7332 (t-100) REVERT: F 67 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: F 70 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8327 (tpp-160) REVERT: F 81 THR cc_start: 0.7806 (m) cc_final: 0.7369 (p) REVERT: F 87 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5765 (mt) REVERT: F 241 GLU cc_start: 0.9050 (mp0) cc_final: 0.8803 (mm-30) REVERT: F 276 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8496 (pp20) outliers start: 80 outliers final: 50 residues processed: 462 average time/residue: 0.1374 time to fit residues: 96.7204 Evaluate side-chains 458 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 395 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 135 THR 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 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 ILE 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 186 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 258 VAL 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 103 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 ASP 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 228 TYR Chi-restraints excluded: chain C residue 230 PHE 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 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 96 VAL 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 264 HIS 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 96 VAL Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 226 GLU 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 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 0.5980 chunk 165 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN E 203 GLN E 233 ASN 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 = 0.4289 r_free = 0.4289 target = 0.179290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122548 restraints weight = 37511.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126199 restraints weight = 16362.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128412 restraints weight = 10437.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129668 restraints weight = 8196.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130218 restraints weight = 7224.769| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18402 Z= 0.248 Angle : 0.923 16.589 25775 Z= 0.472 Chirality : 0.050 0.396 2882 Planarity : 0.005 0.045 2630 Dihedral : 27.375 178.313 3844 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.59 % Favored : 86.18 % Rotamer: Outliers : 5.58 % Allowed : 29.15 % Favored : 65.27 % 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: -2.55 (0.20), residues: 1700 helix: -0.33 (0.18), residues: 808 sheet: -0.94 (0.52), residues: 84 loop : -3.35 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 218 TYR 0.022 0.002 TYR D 228 PHE 0.026 0.002 PHE A 230 TRP 0.054 0.003 TRP A 268 HIS 0.013 0.001 HIS E 243 Details of bonding type rmsd covalent geometry : bond 0.00554 (18386) covalent geometry : angle 0.92017 (25768) hydrogen bonds : bond 0.06346 ( 787) hydrogen bonds : angle 5.51846 ( 2045) metal coordination : bond 0.01621 ( 16) metal coordination : angle 4.58381 ( 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 481 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 397 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8913 (pm20) cc_final: 0.8514 (pp30) REVERT: A 106 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8671 (tm-30) REVERT: A 175 ASP cc_start: 0.8698 (p0) cc_final: 0.8256 (p0) REVERT: A 179 ASP cc_start: 0.8814 (p0) cc_final: 0.8283 (p0) REVERT: B 63 ASP cc_start: 0.8570 (t70) cc_final: 0.8158 (t70) REVERT: B 64 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 128 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: B 170 PHE cc_start: 0.8640 (p90) cc_final: 0.8279 (p90) REVERT: B 178 MET cc_start: 0.7934 (mpp) cc_final: 0.6824 (tpp) REVERT: B 179 ASP cc_start: 0.8425 (p0) cc_final: 0.8197 (p0) REVERT: C 13 GLN cc_start: 0.8918 (pm20) cc_final: 0.8699 (pp30) REVERT: C 51 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6933 (pmt-80) REVERT: C 106 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 133 MET cc_start: 0.8340 (tpp) cc_final: 0.8100 (tpp) REVERT: C 155 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8921 (p) REVERT: C 175 ASP cc_start: 0.8704 (p0) cc_final: 0.8387 (p0) REVERT: C 179 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8229 (p0) REVERT: C 199 HIS cc_start: 0.8456 (m-70) cc_final: 0.8176 (m-70) REVERT: C 228 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7529 (p90) REVERT: C 238 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6426 (mmm160) REVERT: D 99 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8789 (mm-30) REVERT: E 70 ARG cc_start: 0.8885 (ttm-80) cc_final: 0.8395 (tpp-160) REVERT: E 81 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7275 (p) REVERT: E 87 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5799 (mt) REVERT: E 136 LEU cc_start: 0.9348 (mt) cc_final: 0.9081 (mt) REVERT: E 276 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8570 (pp20) REVERT: E 293 TRP cc_start: 0.8247 (t-100) cc_final: 0.7555 (t-100) REVERT: F 67 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: F 70 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8391 (tpp-160) REVERT: F 87 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5917 (mt) REVERT: F 241 GLU cc_start: 0.9080 (mp0) cc_final: 0.8813 (mm-30) REVERT: F 276 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8508 (pp20) outliers start: 84 outliers final: 57 residues processed: 445 average time/residue: 0.1353 time to fit residues: 91.6836 Evaluate side-chains 458 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 390 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 THR 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 64 ILE 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 169 TYR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL 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 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP 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 228 TYR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL 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 221 SER 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 96 VAL 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 289 LEU 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 87 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 GLU 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 Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 49 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 111 optimal weight: 0.0030 chunk 29 optimal weight: 40.0000 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 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 212 GLN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN F 187 HIS F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.182298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128995 restraints weight = 37238.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132654 restraints weight = 17136.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134873 restraints weight = 11043.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136170 restraints weight = 8654.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136741 restraints weight = 7587.295| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18402 Z= 0.178 Angle : 0.897 14.631 25775 Z= 0.454 Chirality : 0.049 0.381 2882 Planarity : 0.005 0.045 2630 Dihedral : 27.172 177.419 3844 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.35 % Favored : 88.41 % Rotamer: Outliers : 4.05 % Allowed : 30.74 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.38 (0.20), residues: 1700 helix: -0.12 (0.19), residues: 776 sheet: -1.07 (0.50), residues: 88 loop : -3.21 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 218 TYR 0.024 0.002 TYR D 228 PHE 0.021 0.002 PHE E 163 TRP 0.060 0.002 TRP A 268 HIS 0.010 0.001 HIS E 243 Details of bonding type rmsd covalent geometry : bond 0.00387 (18386) covalent geometry : angle 0.89599 (25768) hydrogen bonds : bond 0.05630 ( 787) hydrogen bonds : angle 5.37702 ( 2045) metal coordination : bond 0.01383 ( 16) metal coordination : angle 2.84120 ( 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 486 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 425 time to evaluate : 0.633 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: 0.8807 (pm20) cc_final: 0.8442 (pp30) REVERT: A 22 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 106 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 175 ASP cc_start: 0.8533 (p0) cc_final: 0.8085 (p0) REVERT: A 179 ASP cc_start: 0.8631 (p0) cc_final: 0.8131 (p0) REVERT: B 63 ASP cc_start: 0.8391 (t70) cc_final: 0.7956 (t70) REVERT: B 64 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8752 (mt) REVERT: B 128 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: B 131 LEU cc_start: 0.9206 (pp) cc_final: 0.8863 (mm) REVERT: B 170 PHE cc_start: 0.8397 (p90) cc_final: 0.8042 (p90) REVERT: B 178 MET cc_start: 0.7783 (mpp) cc_final: 0.6753 (tpp) REVERT: B 179 ASP cc_start: 0.8217 (p0) cc_final: 0.7752 (p0) REVERT: C 51 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6793 (pmt-80) REVERT: C 92 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6583 (ttpp) REVERT: C 106 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8551 (tm-30) REVERT: C 133 MET cc_start: 0.8166 (tpp) cc_final: 0.7955 (tpp) REVERT: C 155 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8751 (p) REVERT: C 175 ASP cc_start: 0.8508 (p0) cc_final: 0.8155 (p0) REVERT: C 228 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7280 (p90) REVERT: D 99 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8711 (mm-30) REVERT: D 168 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8883 (ptmm) REVERT: D 204 GLN cc_start: 0.8955 (mt0) cc_final: 0.8595 (mt0) REVERT: E 70 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.8362 (tpp-160) REVERT: E 87 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5649 (mt) REVERT: E 136 LEU cc_start: 0.9334 (mt) cc_final: 0.9087 (mt) REVERT: E 183 LYS cc_start: 0.9547 (ttpt) cc_final: 0.9283 (ttpt) REVERT: E 276 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8573 (pp20) REVERT: E 293 TRP cc_start: 0.8175 (t-100) cc_final: 0.7573 (t-100) REVERT: F 70 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8418 (tpp-160) REVERT: F 87 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5548 (mt) REVERT: F 241 GLU cc_start: 0.9025 (mp0) cc_final: 0.8777 (mm-30) REVERT: F 276 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8545 (pp20) outliers start: 61 outliers final: 42 residues processed: 455 average time/residue: 0.1368 time to fit residues: 94.4048 Evaluate side-chains 457 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 406 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL 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 211 LEU Chi-restraints excluded: chain B residue 64 ILE 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 258 VAL 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 92 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 ASP 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 228 TYR Chi-restraints excluded: chain C residue 230 PHE 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 221 SER 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 96 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 226 GLU 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 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 0.0770 chunk 29 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 153 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 66 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN 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 = 0.4325 r_free = 0.4325 target = 0.181213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127835 restraints weight = 37229.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131423 restraints weight = 17153.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133619 restraints weight = 11094.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134826 restraints weight = 8711.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135577 restraints weight = 7669.706| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18402 Z= 0.187 Angle : 0.905 17.992 25775 Z= 0.458 Chirality : 0.050 0.436 2882 Planarity : 0.005 0.047 2630 Dihedral : 27.112 178.111 3844 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.24 % Favored : 87.53 % Rotamer: Outliers : 4.25 % Allowed : 31.34 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.36 (0.20), residues: 1700 helix: -0.16 (0.19), residues: 790 sheet: -1.00 (0.50), residues: 88 loop : -3.19 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 218 TYR 0.022 0.002 TYR D 228 PHE 0.019 0.002 PHE E 163 TRP 0.058 0.002 TRP A 268 HIS 0.010 0.001 HIS E 243 Details of bonding type rmsd covalent geometry : bond 0.00415 (18386) covalent geometry : angle 0.90377 (25768) hydrogen bonds : bond 0.05708 ( 787) hydrogen bonds : angle 5.37952 ( 2045) metal coordination : bond 0.01213 ( 16) metal coordination : angle 3.28540 ( 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 476 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 412 time to evaluate : 0.460 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: 0.8811 (pm20) cc_final: 0.8433 (pp30) REVERT: A 22 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 106 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8578 (tm-30) REVERT: A 175 ASP cc_start: 0.8543 (p0) cc_final: 0.8100 (p0) REVERT: A 179 ASP cc_start: 0.8673 (p0) cc_final: 0.8158 (p0) REVERT: B 63 ASP cc_start: 0.8409 (t70) cc_final: 0.8028 (t70) REVERT: B 64 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8742 (mt) REVERT: B 128 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: B 131 LEU cc_start: 0.9221 (pp) cc_final: 0.8886 (mm) REVERT: B 170 PHE cc_start: 0.8375 (p90) cc_final: 0.8018 (p90) REVERT: B 178 MET cc_start: 0.7817 (mpp) cc_final: 0.6765 (tpp) REVERT: B 179 ASP cc_start: 0.8216 (p0) cc_final: 0.7767 (p0) REVERT: C 51 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6775 (pmt-80) REVERT: C 92 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6530 (ttpp) REVERT: C 106 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8555 (tm-30) REVERT: C 133 MET cc_start: 0.8173 (tpp) cc_final: 0.7969 (tpp) REVERT: C 155 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8819 (p) REVERT: C 175 ASP cc_start: 0.8523 (p0) cc_final: 0.8193 (p0) REVERT: C 228 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7167 (p90) REVERT: D 99 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8717 (mm-30) REVERT: D 168 LYS cc_start: 0.9159 (ttpt) cc_final: 0.8866 (ptmm) REVERT: D 204 GLN cc_start: 0.9037 (mt0) cc_final: 0.8602 (mt0) REVERT: E 70 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8330 (tpp-160) REVERT: E 87 ILE cc_start: 0.6197 (OUTLIER) cc_final: 0.5807 (mt) REVERT: E 136 LEU cc_start: 0.9345 (mt) cc_final: 0.9087 (mt) REVERT: E 169 GLU cc_start: 0.8760 (tp30) cc_final: 0.8418 (mm-30) REVERT: E 276 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8594 (pp20) REVERT: E 293 TRP cc_start: 0.8217 (t-100) cc_final: 0.7634 (t-100) REVERT: F 70 ARG cc_start: 0.8787 (ttm-80) cc_final: 0.8411 (tpp-160) REVERT: F 87 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5555 (mt) REVERT: F 241 GLU cc_start: 0.9043 (mp0) cc_final: 0.8790 (mm-30) REVERT: F 276 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8658 (pp20) outliers start: 64 outliers final: 50 residues processed: 448 average time/residue: 0.1311 time to fit residues: 88.7844 Evaluate side-chains 461 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 402 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL 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 211 LEU 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 128 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 258 VAL 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 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP 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 228 TYR Chi-restraints excluded: chain C residue 230 PHE 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 221 SER 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 96 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 136 optimal weight: 0.0970 chunk 114 optimal weight: 0.3980 chunk 143 optimal weight: 0.0570 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 85 optimal weight: 0.0000 chunk 52 optimal weight: 7.9990 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN F 187 HIS F 203 GLN F 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.186158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133339 restraints weight = 37590.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137208 restraints weight = 16696.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139593 restraints weight = 10547.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140960 restraints weight = 8154.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141737 restraints weight = 7100.536| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 18402 Z= 0.177 Angle : 0.923 17.261 25775 Z= 0.463 Chirality : 0.049 0.406 2882 Planarity : 0.005 0.055 2630 Dihedral : 26.882 177.852 3844 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.29 % Rotamer: Outliers : 3.05 % Allowed : 32.67 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.20 (0.20), residues: 1700 helix: -0.15 (0.19), residues: 788 sheet: -0.88 (0.51), residues: 88 loop : -2.97 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 218 TYR 0.024 0.001 TYR D 228 PHE 0.026 0.002 PHE E 163 TRP 0.062 0.002 TRP A 268 HIS 0.009 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00376 (18386) covalent geometry : angle 0.92227 (25768) hydrogen bonds : bond 0.05296 ( 787) hydrogen bonds : angle 5.37183 ( 2045) metal coordination : bond 0.05519 ( 16) metal coordination : angle 2.57543 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4691.96 seconds wall clock time: 81 minutes 10.14 seconds (4870.14 seconds total)