Starting phenix.real_space_refine on Thu Jul 2 15:31:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjf_65111/07_2026/9vjf_65111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjf_65111/07_2026/9vjf_65111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vjf_65111/07_2026/9vjf_65111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjf_65111/07_2026/9vjf_65111.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjf_65111/07_2026/9vjf_65111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjf_65111/07_2026/9vjf_65111.cif" } resolution = 2.7 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 5627 2.51 5 N 1483 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8819 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1740 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 399 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2189 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'CLR': 2, 'T7M': 1, 'YLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'T7M:plan-3': 1, 'T7M:plan-4': 1, 'T7M:plan-5': 1, 'T7M:plan-6': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 8819 At special positions: 0 Unit cell: (89.38, 117.26, 128.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 2 15.00 O 1644 8.00 N 1483 7.00 C 5627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS R 371 " - pdb=" SG CYS R 375 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 328.9 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 40.2% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.543A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.868A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.523A pdb=" N ARG B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.513A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 330 through 352 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.574A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.068A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 35 through 64 Processing helix chain 'R' and resid 65 through 68 removed outlier: 3.614A pdb=" N GLN R 68 " --> pdb=" O ARG R 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 68' Processing helix chain 'R' and resid 69 through 89 Processing helix chain 'R' and resid 89 through 99 Processing helix chain 'R' and resid 106 through 140 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.572A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 174 Processing helix chain 'R' and resid 192 through 202 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 324 through 368 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 378 through 401 removed outlier: 4.140A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 414 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.602A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.220A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.809A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.030A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.283A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.172A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.904A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.576A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.878A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.233A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.497A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2810 1.34 - 1.46: 2152 1.46 - 1.58: 3949 1.58 - 1.71: 1 1.71 - 1.83: 92 Bond restraints: 9004 Sorted by residual: bond pdb=" O4 T7M R 503 " pdb=" P4 T7M R 503 " ideal model delta sigma weight residual 1.704 1.830 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C4 T7M R 503 " pdb=" O4 T7M R 503 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4 YLX R 504 " pdb=" C5 YLX R 504 " ideal model delta sigma weight residual 1.546 1.494 0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" O13 T7M R 503 " pdb=" P1 T7M R 503 " ideal model delta sigma weight residual 1.659 1.710 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" C7 T7M R 503 " pdb=" O13 T7M R 503 " ideal model delta sigma weight residual 1.411 1.362 0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 8999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 11990 2.22 - 4.44: 194 4.44 - 6.67: 32 6.67 - 8.89: 3 8.89 - 11.11: 2 Bond angle restraints: 12221 Sorted by residual: angle pdb=" N GLU B 25 " pdb=" CA GLU B 25 " pdb=" CB GLU B 25 " ideal model delta sigma weight residual 110.12 115.61 -5.49 1.47e+00 4.63e-01 1.40e+01 angle pdb=" CB MET C 217 " pdb=" CG MET C 217 " pdb=" SD MET C 217 " ideal model delta sigma weight residual 112.70 102.32 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA TYR E 178 " pdb=" CB TYR E 178 " pdb=" CG TYR E 178 " ideal model delta sigma weight residual 113.90 119.72 -5.82 1.80e+00 3.09e-01 1.05e+01 angle pdb=" C VAL E 137 " pdb=" N THR E 138 " pdb=" CA THR E 138 " ideal model delta sigma weight residual 121.59 132.70 -11.11 3.54e+00 7.98e-02 9.85e+00 angle pdb=" C ILE E 177 " pdb=" N TYR E 178 " pdb=" CA TYR E 178 " ideal model delta sigma weight residual 121.81 116.12 5.69 1.83e+00 2.99e-01 9.67e+00 ... (remaining 12216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.61: 5306 29.61 - 59.22: 156 59.22 - 88.83: 18 88.83 - 118.44: 10 118.44 - 148.05: 4 Dihedral angle restraints: 5494 sinusoidal: 2236 harmonic: 3258 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 125.26 54.74 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CB CYS R 371 " pdb=" SG CYS R 371 " pdb=" SG CYS R 375 " pdb=" CB CYS R 375 " ideal model delta sinusoidal sigma weight residual -86.00 -17.63 -68.37 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 159.67 -66.67 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 5491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1189 0.066 - 0.131: 192 0.131 - 0.197: 13 0.197 - 0.263: 4 0.263 - 0.328: 4 Chirality restraints: 1402 Sorted by residual: chirality pdb=" C3 T7M R 503 " pdb=" C2 T7M R 503 " pdb=" C4 T7M R 503 " pdb=" O3 T7M R 503 " both_signs ideal model delta sigma weight residual False 2.37 2.69 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C14 CLR R 501 " pdb=" C13 CLR R 501 " pdb=" C15 CLR R 501 " pdb=" C8 CLR R 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C14 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C15 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.61 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1399 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N YLX R 504 " -0.003 2.00e-02 2.50e+03 8.68e-02 1.13e+02 pdb=" C YLX R 504 " 0.007 2.00e-02 2.50e+03 pdb=" O YLX R 504 " 0.109 2.00e-02 2.50e+03 pdb=" C1 YLX R 504 " -0.106 2.00e-02 2.50e+03 pdb=" C8 YLX R 504 " 0.101 2.00e-02 2.50e+03 pdb=" C9 YLX R 504 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO E 224 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO E 75 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.026 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 140 2.61 - 3.18: 7876 3.18 - 3.75: 14658 3.75 - 4.33: 21752 4.33 - 4.90: 34957 Nonbonded interactions: 79383 Sorted by model distance: nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.031 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.093 3.040 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.096 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.105 3.040 nonbonded pdb=" OE2 GLU C 215 " pdb=" NH1 ARG C 219 " model vdw 2.108 3.120 ... (remaining 79378 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.006 0.126 9007 Z= 0.263 Angle : 0.704 11.109 12227 Z= 0.363 Chirality : 0.051 0.328 1402 Planarity : 0.005 0.087 1522 Dihedral : 15.386 148.049 3383 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1104 helix: 1.30 (0.25), residues: 418 sheet: -0.17 (0.33), residues: 242 loop : -0.61 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 42 TYR 0.029 0.002 TYR E 178 PHE 0.020 0.002 PHE C 234 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 ( 9004) covalent geometry : angle 0.70389 / 0.36 (12221) SS BOND : bond 0.00283 / 0.15 ( 3) SS BOND : angle 0.59476 / 0.28 ( 6) hydrogen bonds : bond 0.17051 / 11.00 ( 483) hydrogen bonds : angle 7.03043 / 4.98 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 26 ASP cc_start: 0.7836 (m-30) cc_final: 0.7635 (m-30) REVERT: C 219 ARG cc_start: 0.7403 (mmt-90) cc_final: 0.6997 (mmt180) REVERT: C 243 THR cc_start: 0.8439 (p) cc_final: 0.8226 (p) REVERT: C 325 MET cc_start: 0.8171 (mmt) cc_final: 0.7902 (mmm) REVERT: D 31 SER cc_start: 0.8200 (m) cc_final: 0.7930 (m) REVERT: R 101 LYS cc_start: 0.8627 (pttm) cc_final: 0.8358 (ptpp) REVERT: R 151 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7129 (tpt170) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.5666 time to fit residues: 105.4740 Evaluate side-chains 140 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 GLN B 346 ASN C 75 GLN E 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117097 restraints weight = 10228.792| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.14 r_work: 0.3308 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9007 Z= 0.178 Angle : 0.603 7.305 12227 Z= 0.318 Chirality : 0.044 0.160 1402 Planarity : 0.005 0.063 1522 Dihedral : 12.262 167.640 1434 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.50 % Allowed : 10.90 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1104 helix: 1.62 (0.25), residues: 418 sheet: -0.47 (0.31), residues: 265 loop : -0.52 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 96 TYR 0.027 0.002 TYR E 178 PHE 0.014 0.002 PHE C 234 TRP 0.023 0.002 TRP C 82 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 9004) covalent geometry : angle 0.60336 / 0.32 (12221) SS BOND : bond 0.00292 / 0.15 ( 3) SS BOND : angle 0.64640 / 0.31 ( 6) hydrogen bonds : bond 0.04369 / 2.84 ( 483) hydrogen bonds : angle 5.65400 / 4.06 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 46 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7335 (ttp80) REVERT: C 219 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7260 (mmt180) REVERT: C 325 MET cc_start: 0.8297 (mmt) cc_final: 0.7938 (mmm) REVERT: D 31 SER cc_start: 0.7957 (m) cc_final: 0.7724 (m) REVERT: E 46 GLU cc_start: 0.8063 (tt0) cc_final: 0.7855 (tt0) REVERT: E 89 GLU cc_start: 0.7952 (mp0) cc_final: 0.7591 (mp0) REVERT: R 101 LYS cc_start: 0.8609 (pttm) cc_final: 0.8220 (ptpp) REVERT: R 151 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.6805 (tpt170) REVERT: R 227 ARG cc_start: 0.7688 (mpt-90) cc_final: 0.7413 (mpt-90) REVERT: R 340 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7466 (mt-10) outliers start: 14 outliers final: 2 residues processed: 163 average time/residue: 0.5262 time to fit residues: 91.1139 Evaluate side-chains 144 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 GLN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116734 restraints weight = 10278.313| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.14 r_work: 0.3304 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9007 Z= 0.186 Angle : 0.579 6.629 12227 Z= 0.303 Chirality : 0.044 0.157 1402 Planarity : 0.005 0.064 1522 Dihedral : 11.318 162.394 1434 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.24 % Allowed : 12.29 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1104 helix: 1.77 (0.25), residues: 417 sheet: -0.66 (0.30), residues: 263 loop : -0.57 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.026 0.002 TYR E 178 PHE 0.013 0.002 PHE C 234 TRP 0.020 0.002 TRP C 82 HIS 0.003 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 9004) covalent geometry : angle 0.57928 / 0.30 (12221) SS BOND : bond 0.00291 / 0.15 ( 3) SS BOND : angle 0.58005 / 0.28 ( 6) hydrogen bonds : bond 0.04169 / 2.70 ( 483) hydrogen bonds : angle 5.40467 / 3.88 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: C 42 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6135 (tmt170) REVERT: C 46 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7273 (ttp80) REVERT: C 186 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: C 219 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7153 (mmt180) REVERT: C 325 MET cc_start: 0.8285 (mmt) cc_final: 0.7918 (mmm) REVERT: D 31 SER cc_start: 0.7971 (m) cc_final: 0.7732 (m) REVERT: E 89 GLU cc_start: 0.7976 (mp0) cc_final: 0.7601 (mp0) REVERT: R 101 LYS cc_start: 0.8622 (pttm) cc_final: 0.8210 (ptpp) REVERT: R 151 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.6786 (tpt170) REVERT: R 227 ARG cc_start: 0.7683 (mpt-90) cc_final: 0.7480 (mpt-90) REVERT: R 333 ARG cc_start: 0.6904 (ttp-170) cc_final: 0.6625 (ttp-170) REVERT: R 337 LEU cc_start: 0.7889 (mm) cc_final: 0.7676 (mm) REVERT: R 340 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7626 (mt-10) outliers start: 21 outliers final: 6 residues processed: 161 average time/residue: 0.5590 time to fit residues: 95.8192 Evaluate side-chains 152 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN B 333 GLN B 346 ASN C 75 GLN C 156 GLN E 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120265 restraints weight = 10463.747| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.02 r_work: 0.3397 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9007 Z= 0.174 Angle : 0.573 7.071 12227 Z= 0.298 Chirality : 0.043 0.165 1402 Planarity : 0.004 0.063 1522 Dihedral : 10.526 157.683 1434 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.56 % Allowed : 13.35 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1104 helix: 1.87 (0.25), residues: 417 sheet: -0.68 (0.30), residues: 260 loop : -0.60 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.025 0.002 TYR E 178 PHE 0.023 0.002 PHE E 68 TRP 0.020 0.002 TRP C 82 HIS 0.003 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 9004) covalent geometry : angle 0.57312 / 0.30 (12221) SS BOND : bond 0.00245 / 0.13 ( 3) SS BOND : angle 0.50905 / 0.25 ( 6) hydrogen bonds : bond 0.03950 / 2.57 ( 483) hydrogen bonds : angle 5.34878 / 3.87 ( 1371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6351 (tmt170) REVERT: C 46 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7467 (ttp80) REVERT: C 186 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: C 325 MET cc_start: 0.8318 (mmt) cc_final: 0.8021 (mmm) REVERT: D 31 SER cc_start: 0.8088 (m) cc_final: 0.7819 (m) REVERT: E 89 GLU cc_start: 0.7998 (mp0) cc_final: 0.7601 (mp0) REVERT: R 101 LYS cc_start: 0.8681 (pttm) cc_final: 0.8295 (ptpp) REVERT: R 151 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.6898 (tpt170) REVERT: R 227 ARG cc_start: 0.7790 (mpt-90) cc_final: 0.7548 (mpt-90) REVERT: R 333 ARG cc_start: 0.7133 (ttp-170) cc_final: 0.6842 (ttp-170) REVERT: R 337 LEU cc_start: 0.8016 (mm) cc_final: 0.7813 (mm) REVERT: R 340 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7656 (mt-10) outliers start: 24 outliers final: 8 residues processed: 158 average time/residue: 0.5402 time to fit residues: 90.6379 Evaluate side-chains 156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 79 optimal weight: 0.0270 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN B 346 ASN C 75 GLN C 132 ASN C 156 GLN C 340 ASN E 82 GLN E 159 ASN E 174 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122728 restraints weight = 10383.081| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.06 r_work: 0.3434 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9007 Z= 0.137 Angle : 0.549 7.361 12227 Z= 0.284 Chirality : 0.042 0.161 1402 Planarity : 0.004 0.061 1522 Dihedral : 9.371 148.322 1434 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.46 % Allowed : 14.64 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1104 helix: 2.16 (0.25), residues: 410 sheet: -0.60 (0.30), residues: 258 loop : -0.58 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 96 TYR 0.021 0.001 TYR E 178 PHE 0.028 0.001 PHE E 68 TRP 0.021 0.001 TRP C 82 HIS 0.003 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9004) covalent geometry : angle 0.54898 / 0.28 (12221) SS BOND : bond 0.00142 / 0.07 ( 3) SS BOND : angle 0.41520 / 0.21 ( 6) hydrogen bonds : bond 0.03689 / 2.41 ( 483) hydrogen bonds : angle 5.16212 / 3.74 ( 1371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 289 GLU cc_start: 0.8281 (pm20) cc_final: 0.8051 (pm20) REVERT: C 46 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7400 (ttp80) REVERT: C 197 ARG cc_start: 0.7309 (mmm160) cc_final: 0.7022 (mmt90) REVERT: C 219 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7368 (mmt180) REVERT: C 325 MET cc_start: 0.8293 (mmt) cc_final: 0.7989 (mmm) REVERT: D 31 SER cc_start: 0.8127 (m) cc_final: 0.7861 (m) REVERT: E 89 GLU cc_start: 0.7973 (mp0) cc_final: 0.7581 (mp0) REVERT: E 171 GLN cc_start: 0.7690 (mt0) cc_final: 0.7041 (tt0) REVERT: R 101 LYS cc_start: 0.8670 (pttm) cc_final: 0.8261 (ptpp) REVERT: R 151 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.6887 (tpt170) REVERT: R 227 ARG cc_start: 0.7815 (mpt-90) cc_final: 0.7542 (mpt-90) REVERT: R 333 ARG cc_start: 0.7060 (ttp-170) cc_final: 0.6783 (ttp-170) REVERT: R 340 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7618 (mt-10) outliers start: 23 outliers final: 8 residues processed: 169 average time/residue: 0.5203 time to fit residues: 93.7893 Evaluate side-chains 152 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN B 346 ASN C 75 GLN C 156 GLN E 82 GLN E 159 ASN E 174 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122097 restraints weight = 10320.548| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.05 r_work: 0.3424 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9007 Z= 0.154 Angle : 0.566 7.500 12227 Z= 0.291 Chirality : 0.043 0.163 1402 Planarity : 0.004 0.061 1522 Dihedral : 8.846 141.773 1434 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.78 % Allowed : 15.49 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1104 helix: 2.14 (0.25), residues: 411 sheet: -0.62 (0.31), residues: 261 loop : -0.55 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 96 TYR 0.022 0.002 TYR E 178 PHE 0.024 0.001 PHE E 68 TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9004) covalent geometry : angle 0.56640 / 0.29 (12221) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.43116 / 0.22 ( 6) hydrogen bonds : bond 0.03712 / 2.41 ( 483) hydrogen bonds : angle 5.15300 / 3.72 ( 1371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 289 GLU cc_start: 0.8319 (pm20) cc_final: 0.8059 (pm20) REVERT: C 46 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7363 (ttp80) REVERT: C 197 ARG cc_start: 0.7392 (mmm160) cc_final: 0.6962 (mmt90) REVERT: C 214 ARG cc_start: 0.7246 (mmt180) cc_final: 0.6867 (mmt180) REVERT: C 219 ARG cc_start: 0.7997 (mmt-90) cc_final: 0.7277 (mmt180) REVERT: C 325 MET cc_start: 0.8323 (mmt) cc_final: 0.8018 (mmm) REVERT: D 21 MET cc_start: 0.6982 (ttt) cc_final: 0.6736 (ttp) REVERT: D 31 SER cc_start: 0.8095 (m) cc_final: 0.7814 (m) REVERT: E 89 GLU cc_start: 0.7943 (mp0) cc_final: 0.7544 (mp0) REVERT: E 171 GLN cc_start: 0.7665 (mt0) cc_final: 0.7025 (tt0) REVERT: E 172 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8574 (m) REVERT: R 101 LYS cc_start: 0.8703 (pttm) cc_final: 0.8274 (ptpp) REVERT: R 151 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.6883 (tpt170) REVERT: R 227 ARG cc_start: 0.7801 (mpt-90) cc_final: 0.7515 (mpt-90) REVERT: R 333 ARG cc_start: 0.7037 (ttp-170) cc_final: 0.6751 (ttp-170) REVERT: R 340 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7634 (mt-10) outliers start: 26 outliers final: 7 residues processed: 168 average time/residue: 0.5353 time to fit residues: 95.8529 Evaluate side-chains 152 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN B 333 GLN B 346 ASN C 75 GLN C 156 GLN E 82 GLN E 159 ASN E 174 GLN R 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123010 restraints weight = 10372.351| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.03 r_work: 0.3432 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9007 Z= 0.145 Angle : 0.559 7.833 12227 Z= 0.288 Chirality : 0.043 0.162 1402 Planarity : 0.004 0.061 1522 Dihedral : 8.501 134.419 1434 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.03 % Allowed : 16.45 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1104 helix: 2.19 (0.25), residues: 413 sheet: -0.62 (0.31), residues: 261 loop : -0.57 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 96 TYR 0.022 0.002 TYR E 178 PHE 0.025 0.001 PHE E 68 TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 9004) covalent geometry : angle 0.55910 / 0.29 (12221) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 0.39041 / 0.19 ( 6) hydrogen bonds : bond 0.03633 / 2.36 ( 483) hydrogen bonds : angle 5.10973 / 3.69 ( 1371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: B 289 GLU cc_start: 0.8338 (pm20) cc_final: 0.8057 (pm20) REVERT: C 46 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7382 (ttp80) REVERT: C 197 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7054 (mmt90) REVERT: C 217 MET cc_start: 0.7566 (ppp) cc_final: 0.7235 (ppp) REVERT: C 219 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7673 (mmm160) REVERT: C 325 MET cc_start: 0.8319 (mmt) cc_final: 0.8013 (mmm) REVERT: D 21 MET cc_start: 0.6911 (ttt) cc_final: 0.6580 (ttp) REVERT: D 31 SER cc_start: 0.8097 (m) cc_final: 0.7817 (m) REVERT: E 89 GLU cc_start: 0.7911 (mp0) cc_final: 0.7524 (mp0) REVERT: E 171 GLN cc_start: 0.7656 (mt0) cc_final: 0.6999 (tt0) REVERT: E 172 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8538 (m) REVERT: E 174 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: R 101 LYS cc_start: 0.8689 (pttm) cc_final: 0.8250 (ptpp) REVERT: R 151 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.6886 (tpt170) REVERT: R 227 ARG cc_start: 0.7776 (mpt-90) cc_final: 0.7495 (mpt-90) REVERT: R 333 ARG cc_start: 0.7020 (ttp-170) cc_final: 0.6772 (ttp-170) REVERT: R 340 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7631 (mt-10) outliers start: 19 outliers final: 9 residues processed: 161 average time/residue: 0.4990 time to fit residues: 85.5955 Evaluate side-chains 157 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.0770 chunk 83 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN C 75 GLN C 156 GLN E 82 GLN E 159 ASN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123341 restraints weight = 10325.561| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.03 r_work: 0.3434 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9007 Z= 0.141 Angle : 0.558 7.929 12227 Z= 0.287 Chirality : 0.042 0.154 1402 Planarity : 0.004 0.060 1522 Dihedral : 8.510 138.632 1434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.03 % Allowed : 16.45 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1104 helix: 2.18 (0.25), residues: 412 sheet: -0.61 (0.31), residues: 260 loop : -0.54 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 96 TYR 0.023 0.002 TYR E 178 PHE 0.023 0.001 PHE E 68 TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9004) covalent geometry : angle 0.55773 / 0.29 (12221) SS BOND : bond 0.00143 / 0.07 ( 3) SS BOND : angle 0.38869 / 0.19 ( 6) hydrogen bonds : bond 0.03600 / 2.35 ( 483) hydrogen bonds : angle 5.09527 / 3.68 ( 1371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 GLU cc_start: 0.8345 (pm20) cc_final: 0.8058 (pm20) REVERT: B 305 CYS cc_start: 0.8293 (t) cc_final: 0.7820 (m) REVERT: C 42 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6312 (tmt170) REVERT: C 46 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7367 (ttp80) REVERT: C 197 ARG cc_start: 0.7423 (mmm160) cc_final: 0.7113 (mmt90) REVERT: C 325 MET cc_start: 0.8331 (mmt) cc_final: 0.8017 (mmm) REVERT: D 31 SER cc_start: 0.8098 (m) cc_final: 0.7820 (m) REVERT: E 89 GLU cc_start: 0.7911 (mp0) cc_final: 0.7536 (mp0) REVERT: E 171 GLN cc_start: 0.7682 (mt0) cc_final: 0.7053 (tt0) REVERT: R 101 LYS cc_start: 0.8681 (pttm) cc_final: 0.8240 (ptpp) REVERT: R 151 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.6883 (tpt170) REVERT: R 227 ARG cc_start: 0.7759 (mpt-90) cc_final: 0.7474 (mpt-90) REVERT: R 333 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6740 (ttp-170) REVERT: R 340 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7614 (mt-10) outliers start: 19 outliers final: 8 residues processed: 160 average time/residue: 0.5152 time to fit residues: 87.7874 Evaluate side-chains 156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.0000 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN C 156 GLN E 159 ASN E 174 GLN R 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126005 restraints weight = 10333.200| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.03 r_work: 0.3466 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9007 Z= 0.122 Angle : 0.554 8.831 12227 Z= 0.284 Chirality : 0.042 0.158 1402 Planarity : 0.004 0.059 1522 Dihedral : 8.352 132.161 1434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.60 % Allowed : 17.31 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1104 helix: 2.27 (0.25), residues: 412 sheet: -0.62 (0.32), residues: 247 loop : -0.57 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 96 TYR 0.020 0.001 TYR B 296 PHE 0.022 0.001 PHE E 68 TRP 0.021 0.001 TRP C 82 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9004) covalent geometry : angle 0.55451 / 0.28 (12221) SS BOND : bond 0.00065 / 0.03 ( 3) SS BOND : angle 0.35451 / 0.18 ( 6) hydrogen bonds : bond 0.03491 / 2.28 ( 483) hydrogen bonds : angle 5.04593 / 3.64 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 289 GLU cc_start: 0.8333 (pm20) cc_final: 0.8045 (pm20) REVERT: B 305 CYS cc_start: 0.8289 (t) cc_final: 0.7843 (m) REVERT: B 308 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7811 (mt-10) REVERT: C 42 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6363 (tmt170) REVERT: C 46 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7422 (ttp80) REVERT: C 219 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7162 (mmm160) REVERT: C 325 MET cc_start: 0.8313 (mmt) cc_final: 0.7996 (mmm) REVERT: E 89 GLU cc_start: 0.7885 (mp0) cc_final: 0.7606 (mp0) REVERT: E 171 GLN cc_start: 0.7673 (mt0) cc_final: 0.7068 (tt0) REVERT: E 172 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8491 (m) REVERT: R 101 LYS cc_start: 0.8684 (pttm) cc_final: 0.8045 (ptpp) REVERT: R 151 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.6883 (tpt170) REVERT: R 227 ARG cc_start: 0.7750 (mpt-90) cc_final: 0.7523 (mpt-90) REVERT: R 333 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6702 (ttp-170) REVERT: R 340 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7620 (mt-10) outliers start: 15 outliers final: 6 residues processed: 164 average time/residue: 0.5161 time to fit residues: 90.4435 Evaluate side-chains 159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN C 156 GLN E 82 GLN E 159 ASN R 72 ASN R 386 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123574 restraints weight = 10360.396| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.03 r_work: 0.3440 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9007 Z= 0.153 Angle : 0.582 11.669 12227 Z= 0.294 Chirality : 0.043 0.171 1402 Planarity : 0.004 0.060 1522 Dihedral : 8.384 127.142 1434 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.39 % Allowed : 17.84 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1104 helix: 2.22 (0.25), residues: 412 sheet: -0.50 (0.31), residues: 266 loop : -0.60 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.023 0.002 TYR B 296 PHE 0.021 0.001 PHE E 68 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9004) covalent geometry : angle 0.58238 / 0.29 (12221) SS BOND : bond 0.00157 / 0.08 ( 3) SS BOND : angle 0.39921 / 0.19 ( 6) hydrogen bonds : bond 0.03619 / 2.36 ( 483) hydrogen bonds : angle 5.12097 / 3.70 ( 1371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 209 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8468 (pptt) REVERT: B 289 GLU cc_start: 0.8350 (pm20) cc_final: 0.8109 (pm20) REVERT: B 305 CYS cc_start: 0.8289 (t) cc_final: 0.7839 (m) REVERT: C 42 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6349 (tmt170) REVERT: C 46 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7367 (ttp80) REVERT: C 212 ASP cc_start: 0.7921 (t0) cc_final: 0.7558 (t0) REVERT: C 217 MET cc_start: 0.7842 (ptm) cc_final: 0.7322 (ppp) REVERT: C 219 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7412 (mmt180) REVERT: C 325 MET cc_start: 0.8351 (mmt) cc_final: 0.8025 (mmm) REVERT: E 89 GLU cc_start: 0.7899 (mp0) cc_final: 0.7608 (mp0) REVERT: E 171 GLN cc_start: 0.7666 (mt0) cc_final: 0.7049 (tt0) REVERT: E 172 SER cc_start: 0.8746 (p) cc_final: 0.8540 (m) REVERT: R 101 LYS cc_start: 0.8708 (pttm) cc_final: 0.8050 (ptpp) REVERT: R 151 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.6894 (tpt170) REVERT: R 227 ARG cc_start: 0.7740 (mpt-90) cc_final: 0.7499 (mpt-90) REVERT: R 340 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7665 (mt-10) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.5581 time to fit residues: 94.0454 Evaluate side-chains 157 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain R residue 69 ASN Chi-restraints excluded: chain R residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN E 159 ASN R 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123666 restraints weight = 10247.852| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.03 r_work: 0.3442 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9007 Z= 0.146 Angle : 0.579 11.239 12227 Z= 0.294 Chirality : 0.043 0.164 1402 Planarity : 0.004 0.060 1522 Dihedral : 8.383 126.539 1434 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.50 % Allowed : 17.95 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1104 helix: 2.20 (0.25), residues: 412 sheet: -0.51 (0.31), residues: 266 loop : -0.59 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 96 TYR 0.027 0.002 TYR B 296 PHE 0.018 0.001 PHE E 68 TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9004) covalent geometry : angle 0.57956 / 0.29 (12221) SS BOND : bond 0.00128 / 0.07 ( 3) SS BOND : angle 0.38138 / 0.18 ( 6) hydrogen bonds : bond 0.03604 / 2.35 ( 483) hydrogen bonds : angle 5.12329 / 3.70 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3576.52 seconds wall clock time: 61 minutes 47.99 seconds (3707.99 seconds total)