Starting phenix.real_space_refine on Fri Aug 22 19:05:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr2_16802/08_2025/8cr2_16802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr2_16802/08_2025/8cr2_16802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cr2_16802/08_2025/8cr2_16802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr2_16802/08_2025/8cr2_16802.map" model { file = "/net/cci-nas-00/data/ceres_data/8cr2_16802/08_2025/8cr2_16802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr2_16802/08_2025/8cr2_16802.cif" } resolution = 4.2 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 306 atoms to isotropic. 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 Zn 1 6.06 5 S 51 5.16 5 C 4419 2.51 5 N 1133 2.21 5 O 1234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6838 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2113 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 16, 'TRANS': 251} Chain breaks: 2 Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2066 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 16, 'TRANS': 245} Chain breaks: 2 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1856 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain breaks: 3 Chain: "B" 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 1658 SG CYS A 289 37.717 41.793 15.466 1.00 88.42 S ATOM 1681 SG CYS A 292 36.187 44.539 16.689 1.00 83.88 S ATOM 3724 SG CYS B 289 39.158 45.820 14.919 1.00 94.34 S ATOM 3747 SG CYS B 292 40.200 43.439 17.412 1.00 83.96 S Time building chain proxies: 1.84, per 1000 atoms: 0.27 Number of scatterers: 6838 At special positions: 0 Unit cell: (74.37, 96.57, 135.42, 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) Zn 1 29.99 S 51 16.00 O 1234 8.00 N 1133 7.00 C 4419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 208 " - pdb=" SG CYS D 284 " 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: 0.60 Conformation dependent library (CDL) restraints added in 352.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 292 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 292 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 289 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 289 " Number of angles added : 6 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 69.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.949A pdb=" N LYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.922A pdb=" N ASP A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 158 removed outlier: 4.132A pdb=" N MET A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 217 through 238 Proline residue: A 227 - end of helix removed outlier: 3.532A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.562A pdb=" N HIS A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.868A pdb=" N LYS B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.775A pdb=" N ASP B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 4.105A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 4.092A pdb=" N LEU B 176 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 178' Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.974A pdb=" N ILE B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Proline residue: B 227 - end of helix removed outlier: 4.137A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 290 through 310 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.681A pdb=" N LEU B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1039 Processing helix chain 'C' and resid 1039 through 1062 removed outlier: 3.820A pdb=" N SER C1047 " --> pdb=" O ALA C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1124 Processing helix chain 'D' and resid 190 through 207 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 214 through 234 removed outlier: 3.520A pdb=" N GLY D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 255 through 284 removed outlier: 3.925A pdb=" N PHE D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 1006 through 1035 removed outlier: 3.969A pdb=" N VAL D1014 " --> pdb=" O ALA D1010 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D1015 " --> pdb=" O TRP D1011 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1035 through 1062 removed outlier: 4.559A pdb=" N LYS D1041 " --> pdb=" O ARG D1037 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D1062 " --> pdb=" O GLN D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1123 removed outlier: 4.752A pdb=" N LYS D1099 " --> pdb=" O ALA D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1161 Processing helix chain 'D' and resid 1162 through 1171 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.565A pdb=" N LEU A 69 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 164 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N THR A 242 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N ASN A 274 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE A 244 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 276 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS A 246 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 273 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL A 316 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 275 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 removed outlier: 6.963A pdb=" N ILE B 40 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP B 39 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE B 245 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 41 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 247 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY B 43 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ILE B 249 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR B 272 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE B 244 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 274 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS B 273 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 316 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 69 removed outlier: 6.008A pdb=" N VAL B 68 " --> pdb=" O PHE B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 429 hydrogen bonds defined for protein. 1278 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: 0.98 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1313 1.33 - 1.45: 1584 1.45 - 1.57: 3997 1.57 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 6975 Sorted by residual: bond pdb=" CA HIS A 323 " pdb=" C HIS A 323 " ideal model delta sigma weight residual 1.522 1.562 -0.041 1.72e-02 3.38e+03 5.62e+00 bond pdb=" CG GLN A 235 " pdb=" CD GLN A 235 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.90e+00 bond pdb=" CG GLN D1112 " pdb=" CD GLN D1112 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.88e+00 bond pdb=" CG GLU C1076 " pdb=" CD GLU C1076 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.23e+00 bond pdb=" CG1 ILE B 249 " pdb=" CD1 ILE B 249 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.12e+00 ... (remaining 6970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 9190 3.09 - 6.18: 194 6.18 - 9.28: 20 9.28 - 12.37: 8 12.37 - 15.46: 1 Bond angle restraints: 9413 Sorted by residual: angle pdb=" CA HIS A 323 " pdb=" C HIS A 323 " pdb=" N GLU A 324 " ideal model delta sigma weight residual 118.59 129.17 -10.58 1.63e+00 3.76e-01 4.21e+01 angle pdb=" N GLU C1076 " pdb=" CA GLU C1076 " pdb=" CB GLU C1076 " ideal model delta sigma weight residual 110.12 118.20 -8.08 1.47e+00 4.63e-01 3.02e+01 angle pdb=" N GLN D1112 " pdb=" CA GLN D1112 " pdb=" CB GLN D1112 " ideal model delta sigma weight residual 110.30 118.33 -8.03 1.54e+00 4.22e-01 2.72e+01 angle pdb=" CB MET D1116 " pdb=" CG MET D1116 " pdb=" SD MET D1116 " ideal model delta sigma weight residual 112.70 128.16 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" CA GLU C1076 " pdb=" CB GLU C1076 " pdb=" CG GLU C1076 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 ... (remaining 9408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3863 17.96 - 35.93: 337 35.93 - 53.89: 48 53.89 - 71.85: 4 71.85 - 89.82: 6 Dihedral angle restraints: 4258 sinusoidal: 1745 harmonic: 2513 Sorted by residual: dihedral pdb=" CB CYS D 208 " pdb=" SG CYS D 208 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual -86.00 -175.82 89.82 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" N GLU C1076 " pdb=" C GLU C1076 " pdb=" CA GLU C1076 " pdb=" CB GLU C1076 " ideal model delta harmonic sigma weight residual 122.80 132.72 -9.92 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CA HIS A 273 " pdb=" C HIS A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 788 0.056 - 0.111: 220 0.111 - 0.167: 60 0.167 - 0.222: 10 0.222 - 0.278: 3 Chirality restraints: 1081 Sorted by residual: chirality pdb=" CA PRO B 169 " pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CB PRO B 169 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA GLU C1076 " pdb=" N GLU C1076 " pdb=" C GLU C1076 " pdb=" CB GLU C1076 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN A 235 " pdb=" N GLN A 235 " pdb=" C GLN A 235 " pdb=" CB GLN A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1078 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1158 " -0.030 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP D1158 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP D1158 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP D1158 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D1158 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D1158 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D1158 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1158 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1158 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D1158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D1011 " -0.027 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP D1011 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP D1011 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP D1011 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D1011 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D1011 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D1011 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1011 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1011 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D1011 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 220 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU D 220 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU D 220 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN D 221 " -0.026 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 43 2.51 - 3.11: 5613 3.11 - 3.71: 10443 3.71 - 4.30: 14029 4.30 - 4.90: 21621 Nonbonded interactions: 51749 Sorted by model distance: nonbonded pdb=" O PHE B 83 " pdb=" OD1 ASP B 84 " model vdw 1.914 3.040 nonbonded pdb=" O LYS D1101 " pdb=" OG SER D1105 " model vdw 2.198 3.040 nonbonded pdb=" O GLN A 235 " pdb=" OG1 THR A 242 " model vdw 2.223 3.040 nonbonded pdb=" O TYR D 277 " pdb=" OG1 THR D 280 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN A 263 " pdb=" NH2 ARG D1077 " model vdw 2.241 3.120 ... (remaining 51744 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 23 through 190 or resid 220 through 344)) selection = (chain 'B' and resid 23 through 344) } 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: 1.130 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3059 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 : 0.004 0.057 6980 Z= 0.216 Angle : 1.141 24.972 9421 Z= 0.598 Chirality : 0.057 0.278 1081 Planarity : 0.007 0.058 1172 Dihedral : 13.243 87.522 2613 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.27), residues: 833 helix: -1.65 (0.19), residues: 535 sheet: -3.24 (0.52), residues: 81 loop : -2.24 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1093 TYR 0.052 0.002 TYR D 224 PHE 0.036 0.002 PHE D1019 TRP 0.083 0.005 TRP D1158 HIS 0.020 0.002 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6975) covalent geometry : angle 1.06773 ( 9413) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.45608 ( 2) hydrogen bonds : bond 0.13592 ( 429) hydrogen bonds : angle 6.04226 ( 1278) metal coordination : bond 0.00651 ( 4) metal coordination : angle 15.98554 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.189 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 103 MET cc_start: -0.2862 (mmm) cc_final: -0.4250 (ptm) REVERT: A 291 MET cc_start: 0.6140 (ptp) cc_final: 0.5606 (ptp) REVERT: B 158 MET cc_start: 0.6750 (mpp) cc_final: 0.6458 (mpp) REVERT: B 326 ARG cc_start: 0.3648 (tpt90) cc_final: 0.1145 (mmp80) REVERT: C 1116 MET cc_start: 0.4065 (ttt) cc_final: 0.3604 (ttt) REVERT: D 222 LEU cc_start: 0.7355 (pp) cc_final: 0.7115 (tp) REVERT: D 259 ARG cc_start: 0.3986 (mtt180) cc_final: 0.2349 (mpt-90) REVERT: D 261 MET cc_start: 0.2969 (ptt) cc_final: 0.1806 (tmm) REVERT: D 270 VAL cc_start: 0.6126 (m) cc_final: 0.4950 (p) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1166 time to fit residues: 31.4242 Evaluate side-chains 122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN C1045 GLN C1064 ASN D1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.216388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165472 restraints weight = 9406.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.164513 restraints weight = 7861.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.164847 restraints weight = 7809.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165214 restraints weight = 6694.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.165603 restraints weight = 6574.734| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.7793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6980 Z= 0.304 Angle : 1.044 19.781 9421 Z= 0.535 Chirality : 0.055 0.213 1081 Planarity : 0.007 0.065 1172 Dihedral : 5.668 22.718 908 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.70 % Allowed : 8.52 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.27), residues: 833 helix: -0.30 (0.20), residues: 536 sheet: -3.79 (0.39), residues: 86 loop : -2.06 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1037 TYR 0.025 0.002 TYR D 230 PHE 0.028 0.004 PHE A 41 TRP 0.048 0.004 TRP D1158 HIS 0.013 0.003 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 6975) covalent geometry : angle 0.99531 ( 9413) SS BOND : bond 0.00667 ( 1) SS BOND : angle 0.94043 ( 2) hydrogen bonds : bond 0.06193 ( 429) hydrogen bonds : angle 5.22909 ( 1278) metal coordination : bond 0.00819 ( 4) metal coordination : angle 12.49439 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 SER cc_start: 0.6168 (m) cc_final: 0.5559 (p) REVERT: A 332 ASN cc_start: 0.7267 (m-40) cc_final: 0.6797 (p0) REVERT: B 332 ASN cc_start: 0.7349 (m110) cc_final: 0.7132 (m110) REVERT: C 1066 MET cc_start: 0.6711 (tmm) cc_final: 0.5224 (mmm) REVERT: C 1079 ILE cc_start: 0.7576 (mm) cc_final: 0.7272 (tp) REVERT: D 217 PHE cc_start: 0.7117 (m-80) cc_final: 0.6649 (m-80) REVERT: D 222 LEU cc_start: 0.7544 (pp) cc_final: 0.7275 (tp) REVERT: D 224 TYR cc_start: 0.6408 (t80) cc_final: 0.5899 (t80) REVERT: D 258 ASN cc_start: 0.7924 (t0) cc_final: 0.7466 (m-40) REVERT: D 259 ARG cc_start: 0.3619 (mtt180) cc_final: 0.2013 (mtm180) REVERT: D 261 MET cc_start: 0.4625 (ptt) cc_final: 0.3489 (tmm) REVERT: D 1022 ASN cc_start: 0.8878 (m110) cc_final: 0.8611 (m110) REVERT: D 1055 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7950 (p0) REVERT: D 1079 ILE cc_start: 0.8386 (pt) cc_final: 0.7896 (pt) outliers start: 13 outliers final: 2 residues processed: 191 average time/residue: 0.0703 time to fit residues: 18.0907 Evaluate side-chains 128 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.209486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.183678 restraints weight = 9625.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.177113 restraints weight = 12275.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171928 restraints weight = 11302.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171468 restraints weight = 12517.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.171262 restraints weight = 10004.629| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.9345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6980 Z= 0.178 Angle : 0.785 15.117 9421 Z= 0.401 Chirality : 0.047 0.192 1081 Planarity : 0.005 0.051 1172 Dihedral : 4.730 19.465 908 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.28), residues: 833 helix: 0.60 (0.21), residues: 536 sheet: -3.41 (0.43), residues: 95 loop : -1.44 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1050 TYR 0.023 0.002 TYR D 230 PHE 0.031 0.002 PHE D1108 TRP 0.046 0.003 TRP D1011 HIS 0.006 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6975) covalent geometry : angle 0.75148 ( 9413) SS BOND : bond 0.00533 ( 1) SS BOND : angle 0.97383 ( 2) hydrogen bonds : bond 0.05196 ( 429) hydrogen bonds : angle 4.63826 ( 1278) metal coordination : bond 0.00517 ( 4) metal coordination : angle 9.04790 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.276 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 29 SER cc_start: 0.6620 (m) cc_final: 0.5983 (p) REVERT: A 264 GLU cc_start: 0.6584 (pt0) cc_final: 0.6130 (pt0) REVERT: B 151 VAL cc_start: 0.7752 (t) cc_final: 0.7532 (t) REVERT: B 230 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7337 (tpm170) REVERT: B 338 LEU cc_start: 0.4058 (mt) cc_final: 0.3322 (mp) REVERT: C 1035 MET cc_start: 0.6946 (ptt) cc_final: 0.6686 (ptt) REVERT: D 259 ARG cc_start: 0.4079 (mtt180) cc_final: 0.1796 (mtm180) REVERT: D 261 MET cc_start: 0.4269 (ptt) cc_final: 0.3269 (tmm) REVERT: D 1079 ILE cc_start: 0.8569 (pt) cc_final: 0.8172 (pt) REVERT: D 1082 MET cc_start: 0.7555 (mmt) cc_final: 0.7333 (mmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0838 time to fit residues: 17.5222 Evaluate side-chains 117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.202878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3955 r_free = 0.3955 target = 0.150040 restraints weight = 9640.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.147605 restraints weight = 11176.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148822 restraints weight = 11242.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148896 restraints weight = 10195.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149102 restraints weight = 9611.903| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 1.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6980 Z= 0.192 Angle : 0.742 11.099 9421 Z= 0.390 Chirality : 0.046 0.172 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.588 16.788 908 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.26 % Allowed : 3.28 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.29), residues: 833 helix: 0.76 (0.21), residues: 536 sheet: -2.77 (0.50), residues: 95 loop : -1.10 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 153 TYR 0.023 0.002 TYR C1072 PHE 0.023 0.002 PHE D1108 TRP 0.044 0.003 TRP D1011 HIS 0.012 0.002 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6975) covalent geometry : angle 0.72672 ( 9413) SS BOND : bond 0.00560 ( 1) SS BOND : angle 0.60247 ( 2) hydrogen bonds : bond 0.05012 ( 429) hydrogen bonds : angle 4.58608 ( 1278) metal coordination : bond 0.00674 ( 4) metal coordination : angle 6.07991 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.7965 (m-80) cc_final: 0.7655 (m-10) REVERT: A 264 GLU cc_start: 0.7031 (pt0) cc_final: 0.6826 (pt0) REVERT: A 304 ASP cc_start: 0.7660 (m-30) cc_final: 0.7396 (m-30) REVERT: B 230 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7352 (tpm170) REVERT: B 305 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6081 (tp40) REVERT: C 1035 MET cc_start: 0.7667 (ptt) cc_final: 0.7426 (ptt) REVERT: D 221 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8623 (pp30) REVERT: D 259 ARG cc_start: 0.4015 (mtt180) cc_final: 0.1895 (mtm180) REVERT: D 261 MET cc_start: 0.4927 (ptt) cc_final: 0.3798 (tmm) REVERT: D 1022 ASN cc_start: 0.8733 (m-40) cc_final: 0.8506 (m110) REVERT: D 1065 MET cc_start: 0.8452 (tpp) cc_final: 0.8126 (mmm) REVERT: D 1082 MET cc_start: 0.7942 (mmt) cc_final: 0.7589 (mmm) REVERT: D 1093 ARG cc_start: 0.7508 (tpt170) cc_final: 0.7163 (tpt170) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.0817 time to fit residues: 16.3098 Evaluate side-chains 118 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.207528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141312 restraints weight = 9631.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142335 restraints weight = 8227.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142774 restraints weight = 7068.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143031 restraints weight = 6717.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144109 restraints weight = 6315.553| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 1.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6980 Z= 0.156 Angle : 0.687 12.628 9421 Z= 0.353 Chirality : 0.044 0.155 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.395 17.005 908 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.39 % Allowed : 2.88 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.29), residues: 833 helix: 0.98 (0.22), residues: 540 sheet: -2.25 (0.54), residues: 90 loop : -0.93 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.024 0.002 TYR D 224 PHE 0.022 0.002 PHE D1108 TRP 0.053 0.003 TRP D1011 HIS 0.006 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6975) covalent geometry : angle 0.66577 ( 9413) SS BOND : bond 0.01585 ( 1) SS BOND : angle 0.70123 ( 2) hydrogen bonds : bond 0.04621 ( 429) hydrogen bonds : angle 4.37645 ( 1278) metal coordination : bond 0.00742 ( 4) metal coordination : angle 6.70407 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.261 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 103 MET cc_start: 0.7858 (tpp) cc_final: 0.7423 (tpp) REVERT: A 264 GLU cc_start: 0.7267 (pt0) cc_final: 0.7058 (pt0) REVERT: A 332 ASN cc_start: 0.7429 (m-40) cc_final: 0.6943 (p0) REVERT: B 230 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7440 (tpm170) REVERT: B 240 GLU cc_start: 0.7796 (tp30) cc_final: 0.7528 (tp30) REVERT: B 291 MET cc_start: 0.8492 (ppp) cc_final: 0.8231 (ppp) REVERT: B 332 ASN cc_start: 0.7954 (m110) cc_final: 0.7601 (m110) REVERT: C 1035 MET cc_start: 0.8049 (ptt) cc_final: 0.7833 (ptt) REVERT: C 1048 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: D 261 MET cc_start: 0.4977 (ptt) cc_final: 0.3882 (tmm) REVERT: D 267 MET cc_start: 0.2243 (mmm) cc_final: 0.1452 (mpp) REVERT: D 1065 MET cc_start: 0.8546 (tpp) cc_final: 0.8320 (mmm) REVERT: D 1082 MET cc_start: 0.7992 (mmt) cc_final: 0.7658 (mmm) outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.0888 time to fit residues: 18.3426 Evaluate side-chains 127 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.200337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.159000 restraints weight = 9665.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.144846 restraints weight = 13219.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140727 restraints weight = 12754.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141788 restraints weight = 11807.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141951 restraints weight = 10406.922| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 1.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6980 Z= 0.162 Angle : 0.707 9.012 9421 Z= 0.367 Chirality : 0.045 0.154 1081 Planarity : 0.004 0.054 1172 Dihedral : 4.400 18.591 908 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.29), residues: 833 helix: 0.90 (0.22), residues: 540 sheet: -2.27 (0.52), residues: 96 loop : -1.01 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1074 TYR 0.020 0.002 TYR D 224 PHE 0.019 0.002 PHE D1108 TRP 0.054 0.003 TRP D1011 HIS 0.004 0.001 HIS D1008 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6975) covalent geometry : angle 0.69653 ( 9413) SS BOND : bond 0.00559 ( 1) SS BOND : angle 0.37664 ( 2) hydrogen bonds : bond 0.04671 ( 429) hydrogen bonds : angle 4.52632 ( 1278) metal coordination : bond 0.00666 ( 4) metal coordination : angle 4.94899 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7007 (tp) cc_final: 0.6396 (tp) REVERT: A 74 ASP cc_start: 0.7282 (t0) cc_final: 0.6970 (t0) REVERT: A 88 SER cc_start: 0.7892 (t) cc_final: 0.7668 (m) REVERT: A 174 LEU cc_start: 0.6953 (tp) cc_final: 0.6638 (tp) REVERT: A 332 ASN cc_start: 0.7094 (m-40) cc_final: 0.6883 (p0) REVERT: B 240 GLU cc_start: 0.7743 (tp30) cc_final: 0.7318 (tp30) REVERT: B 332 ASN cc_start: 0.8087 (m110) cc_final: 0.7790 (m110) REVERT: C 1086 LEU cc_start: 0.7715 (tp) cc_final: 0.7215 (tp) REVERT: D 221 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8447 (mm-40) REVERT: D 261 MET cc_start: 0.5376 (ptt) cc_final: 0.4164 (tmm) REVERT: D 267 MET cc_start: 0.2501 (mmm) cc_final: 0.1572 (mpp) REVERT: D 1065 MET cc_start: 0.8595 (tpp) cc_final: 0.8183 (mmm) REVERT: D 1079 ILE cc_start: 0.8949 (pt) cc_final: 0.8714 (pt) REVERT: D 1082 MET cc_start: 0.8092 (mmt) cc_final: 0.7777 (mmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0740 time to fit residues: 15.8865 Evaluate side-chains 117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 11 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1096 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.201620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142532 restraints weight = 9512.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141786 restraints weight = 9211.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142217 restraints weight = 8305.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142157 restraints weight = 7903.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142273 restraints weight = 7829.815| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 1.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6980 Z= 0.148 Angle : 0.709 7.980 9421 Z= 0.369 Chirality : 0.045 0.182 1081 Planarity : 0.004 0.055 1172 Dihedral : 4.320 17.387 908 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.29), residues: 833 helix: 1.08 (0.22), residues: 539 sheet: -1.83 (0.56), residues: 90 loop : -0.86 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 153 TYR 0.026 0.002 TYR D 210 PHE 0.026 0.002 PHE D 279 TRP 0.090 0.004 TRP D1158 HIS 0.003 0.001 HIS B 273 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6975) covalent geometry : angle 0.69835 ( 9413) SS BOND : bond 0.00474 ( 1) SS BOND : angle 0.26080 ( 2) hydrogen bonds : bond 0.04473 ( 429) hydrogen bonds : angle 4.50399 ( 1278) metal coordination : bond 0.00548 ( 4) metal coordination : angle 4.99120 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.274 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 61 LEU cc_start: 0.7259 (tp) cc_final: 0.6728 (tp) REVERT: A 174 LEU cc_start: 0.7270 (tp) cc_final: 0.6866 (tp) REVERT: A 230 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8573 (ptm-80) REVERT: B 240 GLU cc_start: 0.7610 (tp30) cc_final: 0.7110 (tp30) REVERT: B 306 MET cc_start: 0.8023 (mtp) cc_final: 0.7449 (ttp) REVERT: B 332 ASN cc_start: 0.8266 (m110) cc_final: 0.7861 (m110) REVERT: C 1035 MET cc_start: 0.8216 (ptp) cc_final: 0.7999 (ptp) REVERT: C 1116 MET cc_start: 0.4887 (ttt) cc_final: 0.4606 (ttt) REVERT: D 261 MET cc_start: 0.5607 (ptt) cc_final: 0.4403 (tmm) REVERT: D 267 MET cc_start: 0.3097 (mmm) cc_final: 0.2321 (mpp) REVERT: D 1022 ASN cc_start: 0.8940 (m110) cc_final: 0.8702 (m110) REVERT: D 1082 MET cc_start: 0.8076 (mmt) cc_final: 0.7828 (mmm) REVERT: D 1096 GLN cc_start: 0.7930 (pt0) cc_final: 0.7289 (tp-100) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0786 time to fit residues: 16.0397 Evaluate side-chains 122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 273 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 ASN D1096 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.150195 restraints weight = 9634.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.148618 restraints weight = 14071.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148041 restraints weight = 14815.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145576 restraints weight = 13512.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144799 restraints weight = 13407.867| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 1.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6980 Z= 0.228 Angle : 0.804 8.765 9421 Z= 0.421 Chirality : 0.048 0.206 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.871 22.388 908 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 1.83 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.29), residues: 833 helix: 0.79 (0.22), residues: 534 sheet: -2.21 (0.55), residues: 93 loop : -1.06 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.024 0.003 TYR C1072 PHE 0.024 0.003 PHE A 41 TRP 0.074 0.004 TRP D1158 HIS 0.006 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 6975) covalent geometry : angle 0.79378 ( 9413) SS BOND : bond 0.00365 ( 1) SS BOND : angle 0.42229 ( 2) hydrogen bonds : bond 0.05424 ( 429) hydrogen bonds : angle 4.77127 ( 1278) metal coordination : bond 0.00716 ( 4) metal coordination : angle 5.25283 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7816 (tp) cc_final: 0.7308 (tp) REVERT: A 88 SER cc_start: 0.8463 (t) cc_final: 0.8223 (m) REVERT: A 103 MET cc_start: 0.7805 (tmm) cc_final: 0.7575 (tmm) REVERT: A 153 ARG cc_start: 0.7493 (ttp80) cc_final: 0.7293 (ptp-170) REVERT: A 174 LEU cc_start: 0.7673 (tp) cc_final: 0.7435 (tp) REVERT: A 230 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8456 (ptm-80) REVERT: B 306 MET cc_start: 0.8184 (mtp) cc_final: 0.7952 (mtm) REVERT: B 332 ASN cc_start: 0.8344 (m110) cc_final: 0.7987 (m110) REVERT: C 1065 MET cc_start: 0.8503 (mmp) cc_final: 0.8137 (mmp) REVERT: C 1116 MET cc_start: 0.5026 (ttt) cc_final: 0.4797 (ttt) REVERT: D 261 MET cc_start: 0.5154 (ptt) cc_final: 0.4168 (tmm) REVERT: D 265 SER cc_start: 0.5436 (p) cc_final: 0.5200 (p) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.0735 time to fit residues: 15.8565 Evaluate side-chains 126 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 68 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 172 HIS A 273 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 273 HIS ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.197747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165607 restraints weight = 9669.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156141 restraints weight = 12059.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.154299 restraints weight = 12391.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154461 restraints weight = 12663.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154075 restraints weight = 9490.333| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 1.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6980 Z= 0.160 Angle : 0.752 7.794 9421 Z= 0.401 Chirality : 0.046 0.188 1081 Planarity : 0.005 0.055 1172 Dihedral : 4.562 20.337 908 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.29), residues: 833 helix: 0.94 (0.22), residues: 538 sheet: -2.04 (0.55), residues: 95 loop : -0.75 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.030 0.002 TYR D 228 PHE 0.024 0.002 PHE D1019 TRP 0.103 0.004 TRP D1158 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6975) covalent geometry : angle 0.74550 ( 9413) SS BOND : bond 0.00411 ( 1) SS BOND : angle 0.20938 ( 2) hydrogen bonds : bond 0.04736 ( 429) hydrogen bonds : angle 4.68985 ( 1278) metal coordination : bond 0.00431 ( 4) metal coordination : angle 4.13454 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.346 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 61 LEU cc_start: 0.7863 (tp) cc_final: 0.7595 (tp) REVERT: A 153 ARG cc_start: 0.7297 (ttp80) cc_final: 0.6982 (ptp-170) REVERT: A 174 LEU cc_start: 0.7724 (tp) cc_final: 0.7497 (tp) REVERT: B 306 MET cc_start: 0.8072 (mtp) cc_final: 0.7794 (mtm) REVERT: B 332 ASN cc_start: 0.8246 (m110) cc_final: 0.7956 (m110) REVERT: C 1053 ILE cc_start: 0.8861 (mt) cc_final: 0.8458 (mt) REVERT: C 1072 TYR cc_start: 0.7918 (t80) cc_final: 0.7265 (t80) REVERT: C 1076 GLU cc_start: 0.7513 (mp0) cc_final: 0.7291 (mp0) REVERT: C 1116 MET cc_start: 0.5223 (ttt) cc_final: 0.4996 (ttt) REVERT: D 261 MET cc_start: 0.5216 (ptt) cc_final: 0.4202 (tmm) REVERT: D 265 SER cc_start: 0.5324 (p) cc_final: 0.5057 (p) REVERT: D 1118 SER cc_start: 0.8978 (p) cc_final: 0.8773 (p) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0834 time to fit residues: 16.4965 Evaluate side-chains 127 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN C1058 GLN D1022 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.198758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157545 restraints weight = 9663.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.156557 restraints weight = 13157.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155977 restraints weight = 13767.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 80)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.153479 restraints weight = 11459.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.151088 restraints weight = 13655.549| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 1.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6980 Z= 0.166 Angle : 0.742 7.748 9421 Z= 0.397 Chirality : 0.046 0.157 1081 Planarity : 0.004 0.054 1172 Dihedral : 4.495 19.263 908 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.30), residues: 833 helix: 0.94 (0.22), residues: 540 sheet: -1.92 (0.57), residues: 95 loop : -0.71 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.012 0.002 TYR A 148 PHE 0.026 0.002 PHE D1019 TRP 0.097 0.003 TRP D1158 HIS 0.004 0.001 HIS D1008 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6975) covalent geometry : angle 0.73756 ( 9413) SS BOND : bond 0.00437 ( 1) SS BOND : angle 0.23459 ( 2) hydrogen bonds : bond 0.04751 ( 429) hydrogen bonds : angle 4.69692 ( 1278) metal coordination : bond 0.00476 ( 4) metal coordination : angle 3.19670 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.299 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 153 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6918 (ptp-170) REVERT: B 306 MET cc_start: 0.8050 (mtp) cc_final: 0.7797 (mtm) REVERT: B 332 ASN cc_start: 0.8200 (m110) cc_final: 0.7921 (t0) REVERT: C 1076 GLU cc_start: 0.7503 (mp0) cc_final: 0.6402 (mp0) REVERT: C 1116 MET cc_start: 0.5299 (ttt) cc_final: 0.5096 (ttt) REVERT: D 261 MET cc_start: 0.5212 (ptt) cc_final: 0.4686 (tmm) REVERT: D 1007 ASP cc_start: 0.7023 (p0) cc_final: 0.5797 (p0) REVERT: D 1056 MET cc_start: 0.8154 (ptt) cc_final: 0.7893 (ptt) REVERT: D 1096 GLN cc_start: 0.7191 (pt0) cc_final: 0.6829 (tp-100) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0870 time to fit residues: 17.7246 Evaluate side-chains 129 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1096 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.196580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.168291 restraints weight = 9692.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.149209 restraints weight = 11460.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147534 restraints weight = 17972.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.148055 restraints weight = 15784.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147943 restraints weight = 11936.534| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 1.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6980 Z= 0.182 Angle : 0.761 7.556 9421 Z= 0.409 Chirality : 0.047 0.157 1081 Planarity : 0.005 0.055 1172 Dihedral : 4.612 19.958 908 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.30), residues: 833 helix: 0.87 (0.22), residues: 541 sheet: -2.04 (0.57), residues: 94 loop : -0.63 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.019 0.002 TYR D 210 PHE 0.027 0.002 PHE D1019 TRP 0.094 0.005 TRP D1158 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6975) covalent geometry : angle 0.75832 ( 9413) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.58499 ( 2) hydrogen bonds : bond 0.04847 ( 429) hydrogen bonds : angle 4.72890 ( 1278) metal coordination : bond 0.00400 ( 4) metal coordination : angle 2.77425 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.54 seconds wall clock time: 24 minutes 9.42 seconds (1449.42 seconds total)