Starting phenix.real_space_refine on Tue Mar 3 15:11:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ged_29966/03_2026/8ged_29966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ged_29966/03_2026/8ged_29966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2026/8ged_29966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2026/8ged_29966.map" model { file = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2026/8ged_29966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2026/8ged_29966.cif" } resolution = 3.5 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= -0.001 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4179 2.51 5 N 1142 2.21 5 O 1147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6505 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1885 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 14, 'ASN:plan1': 8, 'GLU:plan': 20, 'ASP:plan': 14, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 271 Chain: "B" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2332 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 6, 'GLU:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 17, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 182 Chain: "G" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 301 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1972 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 6, 'ASP:plan': 5, 'ASN:plan1': 4, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.23 Number of scatterers: 6505 At special positions: 0 Unit cell: (71.02, 97.52, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1147 8.00 N 1142 7.00 C 4179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 0.61 Conformation dependent library (CDL) restraints added in 246.6 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 50.4% alpha, 16.1% 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 12 through 40 removed outlier: 3.651A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.069A pdb=" N ASN A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.385A pdb=" N ASN A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.446A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.993A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.217A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.745A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.900A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.345A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.191A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.597A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.907A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.600A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.906A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.970A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.508A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.841A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.161A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.346A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.780A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.516A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.735A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.579A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.870A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1161 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: 0.99 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2140 1.34 - 1.46: 1724 1.46 - 1.58: 2732 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 6644 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.580 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.453 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.570 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.492 -0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 6639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 9018 1.74 - 3.49: 78 3.49 - 5.23: 15 5.23 - 6.98: 2 6.98 - 8.72: 1 Bond angle restraints: 9114 Sorted by residual: angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 125.02 -8.72 3.50e+00 8.16e-02 6.21e+00 angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 108.46 111.90 -3.44 1.51e+00 4.39e-01 5.19e+00 angle pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " pdb=" CD2 LEU A 46 " ideal model delta sigma weight residual 110.70 104.13 6.57 3.00e+00 1.11e-01 4.79e+00 angle pdb=" N ASP B 258 " pdb=" CA ASP B 258 " pdb=" C ASP B 258 " ideal model delta sigma weight residual 113.56 110.67 2.89 1.39e+00 5.18e-01 4.32e+00 angle pdb=" N GLY B 244 " pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 113.02 110.05 2.97 1.59e+00 3.96e-01 3.50e+00 ... (remaining 9109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 3438 14.10 - 28.20: 260 28.20 - 42.30: 92 42.30 - 56.40: 15 56.40 - 70.50: 5 Dihedral angle restraints: 3810 sinusoidal: 1049 harmonic: 2761 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N LEU B 69 " pdb=" CA LEU B 69 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA THR B 65 " pdb=" C THR B 65 " pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 798 0.037 - 0.075: 224 0.075 - 0.112: 64 0.112 - 0.150: 11 0.150 - 0.187: 2 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1096 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ILE R 277 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 236 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 233 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C LYS A 233 " 0.018 2.00e-02 2.50e+03 pdb=" O LYS A 233 " -0.007 2.00e-02 2.50e+03 pdb=" N TRP A 234 " -0.006 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1395 2.78 - 3.31: 6296 3.31 - 3.84: 10884 3.84 - 4.37: 11330 4.37 - 4.90: 20841 Nonbonded interactions: 50746 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.332 3.120 nonbonded pdb=" OG1 THR B 249 " pdb=" OG1 THR B 263 " model vdw 2.338 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.347 3.040 nonbonded pdb=" OG SER B 201 " pdb=" NE1 TRP B 211 " model vdw 2.364 3.120 ... (remaining 50741 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=0.00 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.970 Find NCS groups from input model: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.003 0.057 6646 Z= 0.131 Angle : 0.475 8.721 9118 Z= 0.252 Chirality : 0.039 0.187 1099 Planarity : 0.003 0.031 1163 Dihedral : 12.401 70.496 2010 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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 are not related in a simple way. whole: 1.82 (0.28), residues: 928 helix: 2.97 (0.25), residues: 415 sheet: -0.04 (0.42), residues: 147 loop : -0.34 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.006 0.001 TYR B 105 PHE 0.008 0.001 PHE R 133 TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6644) covalent geometry : angle 0.47504 ( 9114) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.73948 ( 4) hydrogen bonds : bond 0.15187 ( 402) hydrogen bonds : angle 6.26684 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.282 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0527 time to fit residues: 8.4143 Evaluate side-chains 81 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0050 chunk 74 optimal weight: 0.3980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.151788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131310 restraints weight = 9851.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.134854 restraints weight = 5200.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137218 restraints weight = 3344.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.138646 restraints weight = 2435.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.139769 restraints weight = 1962.006| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6646 Z= 0.129 Angle : 0.482 6.351 9118 Z= 0.260 Chirality : 0.041 0.167 1099 Planarity : 0.003 0.030 1163 Dihedral : 4.096 16.575 1013 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.78 % Allowed : 12.43 % Favored : 85.80 % 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 are not related in a simple way. whole: 2.04 (0.28), residues: 928 helix: 2.97 (0.25), residues: 422 sheet: 0.18 (0.40), residues: 152 loop : -0.10 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.010 0.001 TYR R 199 PHE 0.016 0.001 PHE R 193 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6644) covalent geometry : angle 0.48123 ( 9114) SS BOND : bond 0.00563 ( 2) SS BOND : angle 0.94636 ( 4) hydrogen bonds : bond 0.03695 ( 402) hydrogen bonds : angle 4.56113 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8029 (mmt) cc_final: 0.7501 (mmt) REVERT: B 237 ASN cc_start: 0.8655 (t0) cc_final: 0.8420 (t0) REVERT: R 82 MET cc_start: 0.6076 (ttm) cc_final: 0.5817 (ttp) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.0488 time to fit residues: 7.1143 Evaluate side-chains 87 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 111 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.128466 restraints weight = 9949.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131944 restraints weight = 5312.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134255 restraints weight = 3462.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135673 restraints weight = 2542.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136795 restraints weight = 2061.547| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6646 Z= 0.136 Angle : 0.474 5.843 9118 Z= 0.255 Chirality : 0.041 0.194 1099 Planarity : 0.003 0.030 1163 Dihedral : 4.028 16.964 1013 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.96 % Allowed : 14.60 % Favored : 82.45 % 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 are not related in a simple way. whole: 1.98 (0.28), residues: 928 helix: 2.85 (0.25), residues: 428 sheet: 0.00 (0.40), residues: 159 loop : 0.00 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.011 0.001 TYR B 59 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6644) covalent geometry : angle 0.47384 ( 9114) SS BOND : bond 0.00528 ( 2) SS BOND : angle 0.92493 ( 4) hydrogen bonds : bond 0.03572 ( 402) hydrogen bonds : angle 4.27885 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.8051 (mmt) cc_final: 0.7588 (mmt) REVERT: B 75 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7561 (mm110) REVERT: B 237 ASN cc_start: 0.8585 (t0) cc_final: 0.8350 (t0) outliers start: 15 outliers final: 14 residues processed: 96 average time/residue: 0.0463 time to fit residues: 7.0622 Evaluate side-chains 97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128317 restraints weight = 9957.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131781 restraints weight = 5316.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.134100 restraints weight = 3456.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.135703 restraints weight = 2544.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136657 restraints weight = 2031.322| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6646 Z= 0.127 Angle : 0.471 6.250 9118 Z= 0.253 Chirality : 0.040 0.149 1099 Planarity : 0.003 0.029 1163 Dihedral : 4.045 19.186 1013 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.75 % Allowed : 14.99 % Favored : 81.26 % 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 are not related in a simple way. whole: 1.97 (0.29), residues: 928 helix: 2.78 (0.25), residues: 430 sheet: -0.06 (0.40), residues: 165 loop : 0.11 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.009 0.001 TYR R 199 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6644) covalent geometry : angle 0.46792 ( 9114) SS BOND : bond 0.00850 ( 2) SS BOND : angle 2.75368 ( 4) hydrogen bonds : bond 0.03408 ( 402) hydrogen bonds : angle 4.21010 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.228 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.0451 time to fit residues: 7.0778 Evaluate side-chains 95 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.139682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118727 restraints weight = 10698.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122007 restraints weight = 5928.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124151 restraints weight = 3931.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125775 restraints weight = 2951.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126652 restraints weight = 2365.318| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6646 Z= 0.151 Angle : 0.480 5.821 9118 Z= 0.258 Chirality : 0.041 0.147 1099 Planarity : 0.003 0.030 1163 Dihedral : 4.145 20.937 1013 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.34 % Allowed : 16.37 % Favored : 79.29 % 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 are not related in a simple way. whole: 1.84 (0.29), residues: 928 helix: 2.73 (0.25), residues: 430 sheet: -0.35 (0.39), residues: 167 loop : 0.11 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.018 0.001 TYR B 59 PHE 0.012 0.001 PHE B 235 TRP 0.008 0.001 TRP B 211 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6644) covalent geometry : angle 0.47746 ( 9114) SS BOND : bond 0.00487 ( 2) SS BOND : angle 2.20625 ( 4) hydrogen bonds : bond 0.03534 ( 402) hydrogen bonds : angle 4.18275 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8697 (t0) cc_final: 0.8440 (t0) outliers start: 22 outliers final: 18 residues processed: 97 average time/residue: 0.0489 time to fit residues: 7.5040 Evaluate side-chains 98 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.121199 restraints weight = 10998.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124597 restraints weight = 6056.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126918 restraints weight = 4006.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.128458 restraints weight = 2968.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129625 restraints weight = 2385.263| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6646 Z= 0.123 Angle : 0.461 7.035 9118 Z= 0.246 Chirality : 0.040 0.145 1099 Planarity : 0.003 0.030 1163 Dihedral : 4.070 20.623 1013 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.34 % Allowed : 16.37 % Favored : 79.29 % 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 are not related in a simple way. whole: 1.75 (0.29), residues: 928 helix: 2.66 (0.25), residues: 436 sheet: -0.38 (0.39), residues: 166 loop : -0.00 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.012 0.001 TYR B 59 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP R 313 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6644) covalent geometry : angle 0.46023 ( 9114) SS BOND : bond 0.00423 ( 2) SS BOND : angle 1.67508 ( 4) hydrogen bonds : bond 0.03337 ( 402) hydrogen bonds : angle 4.03803 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7947 (t0) REVERT: R 107 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7022 (mm-30) REVERT: R 174 TYR cc_start: 0.8251 (p90) cc_final: 0.7883 (p90) outliers start: 22 outliers final: 18 residues processed: 100 average time/residue: 0.0431 time to fit residues: 6.7780 Evaluate side-chains 102 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 76 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122098 restraints weight = 10861.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125465 restraints weight = 5980.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.127776 restraints weight = 3966.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.129277 restraints weight = 2939.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130334 restraints weight = 2369.595| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6646 Z= 0.112 Angle : 0.455 7.479 9118 Z= 0.242 Chirality : 0.040 0.145 1099 Planarity : 0.003 0.029 1163 Dihedral : 4.043 20.037 1013 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.55 % Allowed : 17.55 % Favored : 78.90 % 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 are not related in a simple way. whole: 1.76 (0.29), residues: 928 helix: 2.70 (0.25), residues: 436 sheet: -0.41 (0.39), residues: 161 loop : -0.03 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.010 0.001 TYR B 59 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6644) covalent geometry : angle 0.45406 ( 9114) SS BOND : bond 0.00355 ( 2) SS BOND : angle 1.44993 ( 4) hydrogen bonds : bond 0.03211 ( 402) hydrogen bonds : angle 3.97367 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.168 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 17 residues processed: 98 average time/residue: 0.0469 time to fit residues: 7.3048 Evaluate side-chains 97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 53 optimal weight: 0.0770 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.124223 restraints weight = 10890.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127625 restraints weight = 5977.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.129910 restraints weight = 3928.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131513 restraints weight = 2908.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132608 restraints weight = 2311.482| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6646 Z= 0.095 Angle : 0.438 6.415 9118 Z= 0.234 Chirality : 0.039 0.144 1099 Planarity : 0.003 0.030 1163 Dihedral : 3.900 19.372 1013 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.54 % Allowed : 17.16 % Favored : 78.30 % 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 are not related in a simple way. whole: 1.84 (0.29), residues: 928 helix: 2.87 (0.25), residues: 429 sheet: -0.32 (0.39), residues: 156 loop : -0.15 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.009 0.001 TYR R 316 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP R 313 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 6644) covalent geometry : angle 0.43720 ( 9114) SS BOND : bond 0.00263 ( 2) SS BOND : angle 1.29318 ( 4) hydrogen bonds : bond 0.03009 ( 402) hydrogen bonds : angle 3.84103 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.8196 (mmt) cc_final: 0.7757 (mmt) REVERT: B 155 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7845 (t0) outliers start: 23 outliers final: 18 residues processed: 98 average time/residue: 0.0410 time to fit residues: 6.3607 Evaluate side-chains 99 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122453 restraints weight = 11007.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125777 restraints weight = 6070.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128078 restraints weight = 4025.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129575 restraints weight = 2983.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130768 restraints weight = 2404.042| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6646 Z= 0.118 Angle : 0.454 6.304 9118 Z= 0.242 Chirality : 0.040 0.144 1099 Planarity : 0.003 0.029 1163 Dihedral : 3.939 18.579 1013 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.55 % Allowed : 18.34 % Favored : 78.11 % 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 are not related in a simple way. whole: 1.79 (0.29), residues: 928 helix: 2.82 (0.25), residues: 430 sheet: -0.49 (0.39), residues: 161 loop : -0.08 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.011 0.001 TYR B 59 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP B 339 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6644) covalent geometry : angle 0.45343 ( 9114) SS BOND : bond 0.00349 ( 2) SS BOND : angle 1.33275 ( 4) hydrogen bonds : bond 0.03124 ( 402) hydrogen bonds : angle 3.88753 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.8296 (mmt) cc_final: 0.7898 (mmt) REVERT: B 155 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7869 (t0) outliers start: 18 outliers final: 17 residues processed: 92 average time/residue: 0.0438 time to fit residues: 6.5703 Evaluate side-chains 94 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121655 restraints weight = 10890.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.124951 restraints weight = 6062.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127214 restraints weight = 4033.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128602 restraints weight = 2999.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.129394 restraints weight = 2444.530| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6646 Z= 0.129 Angle : 0.461 6.143 9118 Z= 0.246 Chirality : 0.040 0.142 1099 Planarity : 0.003 0.029 1163 Dihedral : 3.998 18.079 1013 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.94 % Allowed : 17.95 % Favored : 78.11 % 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 are not related in a simple way. whole: 1.76 (0.29), residues: 928 helix: 2.81 (0.25), residues: 430 sheet: -0.52 (0.39), residues: 161 loop : -0.10 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.013 0.001 TYR B 59 PHE 0.014 0.001 PHE B 199 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6644) covalent geometry : angle 0.45981 ( 9114) SS BOND : bond 0.00388 ( 2) SS BOND : angle 1.33345 ( 4) hydrogen bonds : bond 0.03229 ( 402) hydrogen bonds : angle 3.91929 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.8313 (mmt) cc_final: 0.7906 (mmt) REVERT: B 155 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7823 (t0) outliers start: 20 outliers final: 18 residues processed: 91 average time/residue: 0.0439 time to fit residues: 6.4749 Evaluate side-chains 97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 65 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.142089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121404 restraints weight = 10567.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124755 restraints weight = 5808.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126994 restraints weight = 3843.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128539 restraints weight = 2841.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.129437 restraints weight = 2283.111| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6646 Z= 0.105 Angle : 0.440 6.112 9118 Z= 0.235 Chirality : 0.040 0.143 1099 Planarity : 0.003 0.029 1163 Dihedral : 3.906 18.026 1013 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.55 % Allowed : 18.34 % Favored : 78.11 % 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 are not related in a simple way. whole: 1.81 (0.28), residues: 928 helix: 2.87 (0.25), residues: 428 sheet: -0.30 (0.39), residues: 154 loop : -0.20 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.009 0.001 TYR R 316 PHE 0.011 0.001 PHE B 199 TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6644) covalent geometry : angle 0.43946 ( 9114) SS BOND : bond 0.00304 ( 2) SS BOND : angle 1.19587 ( 4) hydrogen bonds : bond 0.03044 ( 402) hydrogen bonds : angle 3.83002 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1101.60 seconds wall clock time: 19 minutes 35.22 seconds (1175.22 seconds total)