Starting phenix.real_space_refine on Fri Aug 22 18:34:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8orj_17127/08_2025/8orj_17127_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orj_17127/08_2025/8orj_17127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8orj_17127/08_2025/8orj_17127_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orj_17127/08_2025/8orj_17127_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8orj_17127/08_2025/8orj_17127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orj_17127/08_2025/8orj_17127.map" } resolution = 3.3 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= 0.007 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 4372 2.51 5 N 1188 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 6930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3521 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 441} Chain breaks: 1 Chain: "B" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3310 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FDA': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 904 SG CYS A 122 38.366 31.493 70.225 1.00 51.16 S ATOM 904 SG CYS A 122 38.366 31.493 70.225 1.00 51.16 S Time building chain proxies: 1.98, per 1000 atoms: 0.29 Number of scatterers: 6930 At special positions: 0 Unit cell: (75.4, 77.35, 111.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 4 15.00 Mg 2 11.99 O 1314 8.00 N 1188 7.00 C 4372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 324.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 36.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.793A pdb=" N GLN A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 56 removed outlier: 3.736A pdb=" N LYS A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 50 " --> pdb=" O MET A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.758A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 208 through 219 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 264 through 284 removed outlier: 3.859A pdb=" N LYS A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 336 Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 133 through 145 Processing helix chain 'B' and resid 156 through 166 removed outlier: 4.129A pdb=" N TYR B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 3.572A pdb=" N LYS B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.957A pdb=" N HIS B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 396 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 467 through 478 Processing helix chain 'B' and resid 481 through 490 removed outlier: 6.322A pdb=" N GLU B 486 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 488 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 489 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.646A pdb=" N CYS A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N ILE A 83 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N PHE A 102 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N LEU A 85 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 11.450A pdb=" N ALA A 100 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N ASP A 87 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN A 98 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 98 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 375 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 374 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.694A pdb=" N VAL A 347 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 128 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 349 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG A 125 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N SER A 260 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU A 127 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE A 258 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR A 129 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL A 256 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU A 131 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN A 253 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 233 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP A 235 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 497 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 91 removed outlier: 3.768A pdb=" N GLN B 89 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 129 removed outlier: 5.907A pdb=" N LEU B 129 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 151 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 171 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU B 258 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP B 173 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.847A pdb=" N LYS B 265 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 298 " --> pdb=" O CYS B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.030A pdb=" N LEU B 340 " --> pdb=" O THR B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 409 through 414 removed outlier: 4.249A pdb=" N LYS B 418 " --> pdb=" O GLY B 463 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 813 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: 0.82 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1389 1.33 - 1.45: 1641 1.45 - 1.57: 3954 1.57 - 1.70: 8 1.70 - 1.82: 80 Bond restraints: 7072 Sorted by residual: bond pdb=" N ILE B 255 " pdb=" CA ILE B 255 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.14e-02 7.69e+03 1.48e+01 bond pdb=" N ILE A 500 " pdb=" CA ILE A 500 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.06e-02 8.90e+03 1.37e+01 bond pdb=" N GLU B 468 " pdb=" CA GLU B 468 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" CZ ARG A 263 " pdb=" NH2 ARG A 263 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N THR A 129 " pdb=" CA THR A 129 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.21e-02 6.83e+03 1.11e+01 ... (remaining 7067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6483 1.64 - 3.28: 2483 3.28 - 4.91: 506 4.91 - 6.55: 78 6.55 - 8.19: 14 Bond angle restraints: 9564 Sorted by residual: angle pdb=" CA LYS A 496 " pdb=" C LYS A 496 " pdb=" O LYS A 496 " ideal model delta sigma weight residual 121.11 113.88 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" CB HIS A 150 " pdb=" CG HIS A 150 " pdb=" CD2 HIS A 150 " ideal model delta sigma weight residual 131.20 124.03 7.17 1.30e+00 5.92e-01 3.04e+01 angle pdb=" CB HIS B 32 " pdb=" CG HIS B 32 " pdb=" CD2 HIS B 32 " ideal model delta sigma weight residual 131.20 124.28 6.92 1.30e+00 5.92e-01 2.83e+01 angle pdb=" CA GLY A 123 " pdb=" C GLY A 123 " pdb=" O GLY A 123 " ideal model delta sigma weight residual 121.38 116.40 4.98 9.40e-01 1.13e+00 2.81e+01 angle pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.00e+00 1.00e+00 2.71e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3794 17.80 - 35.60: 327 35.60 - 53.39: 96 53.39 - 71.19: 36 71.19 - 88.99: 10 Dihedral angle restraints: 4263 sinusoidal: 1767 harmonic: 2496 Sorted by residual: dihedral pdb=" CA PHE A 118 " pdb=" C PHE A 118 " pdb=" N ASP A 119 " pdb=" CA ASP A 119 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLN B 89 " pdb=" C GLN B 89 " pdb=" N LEU B 90 " pdb=" CA LEU B 90 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" C LEU A 42 " pdb=" N LEU A 42 " pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " ideal model delta harmonic sigma weight residual -122.60 -133.96 11.36 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 4260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 554 0.070 - 0.140: 332 0.140 - 0.210: 128 0.210 - 0.280: 25 0.280 - 0.350: 7 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA LEU A 42 " pdb=" N LEU A 42 " pdb=" C LEU A 42 " pdb=" CB LEU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA MET B 346 " pdb=" N MET B 346 " pdb=" C MET B 346 " pdb=" CB MET B 346 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA THR A 484 " pdb=" N THR A 484 " pdb=" C THR A 484 " pdb=" CB THR A 484 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1043 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FDA B 602 " 0.405 2.00e-02 2.50e+03 1.74e-01 1.44e+03 pdb=" C10 FDA B 602 " 0.060 2.00e-02 2.50e+03 pdb=" C2 FDA B 602 " -0.182 2.00e-02 2.50e+03 pdb=" C4 FDA B 602 " 0.019 2.00e-02 2.50e+03 pdb=" C4X FDA B 602 " 0.111 2.00e-02 2.50e+03 pdb=" C5X FDA B 602 " 0.134 2.00e-02 2.50e+03 pdb=" C6 FDA B 602 " 0.065 2.00e-02 2.50e+03 pdb=" C7 FDA B 602 " -0.067 2.00e-02 2.50e+03 pdb=" C7M FDA B 602 " -0.150 2.00e-02 2.50e+03 pdb=" C8 FDA B 602 " -0.122 2.00e-02 2.50e+03 pdb=" C8M FDA B 602 " -0.261 2.00e-02 2.50e+03 pdb=" C9 FDA B 602 " -0.048 2.00e-02 2.50e+03 pdb=" C9A FDA B 602 " 0.082 2.00e-02 2.50e+03 pdb=" N1 FDA B 602 " -0.084 2.00e-02 2.50e+03 pdb=" N10 FDA B 602 " 0.171 2.00e-02 2.50e+03 pdb=" N3 FDA B 602 " -0.122 2.00e-02 2.50e+03 pdb=" N5 FDA B 602 " 0.263 2.00e-02 2.50e+03 pdb=" O2 FDA B 602 " -0.315 2.00e-02 2.50e+03 pdb=" O4 FDA B 602 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 601 " 0.174 2.00e-02 2.50e+03 1.26e-01 3.18e+02 pdb=" C2N NAD B 601 " -0.268 2.00e-02 2.50e+03 pdb=" C3N NAD B 601 " -0.037 2.00e-02 2.50e+03 pdb=" C4N NAD B 601 " 0.051 2.00e-02 2.50e+03 pdb=" C5N NAD B 601 " 0.017 2.00e-02 2.50e+03 pdb=" C6N NAD B 601 " -0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 601 " 0.133 2.00e-02 2.50e+03 pdb=" N1N NAD B 601 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 239 " 0.104 2.00e-02 2.50e+03 5.01e-02 6.26e+01 pdb=" CG TRP B 239 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 239 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 239 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP B 239 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP B 239 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 239 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 239 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 239 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 239 " 0.046 2.00e-02 2.50e+03 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 12 2.51 - 3.11: 4725 3.11 - 3.71: 10441 3.71 - 4.30: 15330 4.30 - 4.90: 25231 Nonbonded interactions: 55739 Sorted by model distance: nonbonded pdb=" OD2 ASP A 119 " pdb="MG MG A 602 " model vdw 1.914 2.170 nonbonded pdb=" OD2 ASP B 500 " pdb="MG MG A 602 " model vdw 1.993 2.170 nonbonded pdb=" NE2 HIS A 353 " pdb="MG MG A 601 " model vdw 2.023 2.250 nonbonded pdb=" NE2 HIS A 259 " pdb="MG MG A 601 " model vdw 2.054 2.250 nonbonded pdb=" SG CYS A 122 " pdb="MG MG A 601 " model vdw 2.064 2.530 ... (remaining 55734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.010 Find NCS groups from input model: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.012 0.060 7072 Z= 0.763 Angle : 1.751 8.188 9564 Z= 1.208 Chirality : 0.098 0.350 1046 Planarity : 0.012 0.174 1227 Dihedral : 16.332 88.988 2669 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.16 % Allowed : 9.63 % Favored : 87.21 % Cbeta Deviations : 0.13 % 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: -0.70 (0.27), residues: 870 helix: -0.12 (0.28), residues: 281 sheet: -0.91 (0.38), residues: 172 loop : -0.34 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.088 0.013 TYR B 484 PHE 0.076 0.012 PHE B 332 TRP 0.104 0.018 TRP B 239 HIS 0.015 0.004 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.01169 ( 7072) covalent geometry : angle 1.75113 ( 9564) hydrogen bonds : bond 0.19053 ( 293) hydrogen bonds : angle 8.41161 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: A 363 VAL cc_start: 0.8715 (t) cc_final: 0.8482 (t) REVERT: A 371 LEU cc_start: 0.8285 (tp) cc_final: 0.7961 (tp) REVERT: B 165 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 240 HIS cc_start: 0.7058 (p-80) cc_final: 0.6126 (p-80) REVERT: B 384 TRP cc_start: 0.7699 (t60) cc_final: 0.6964 (t60) outliers start: 23 outliers final: 8 residues processed: 304 average time/residue: 0.1002 time to fit residues: 38.6912 Evaluate side-chains 160 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 29 ASN A 232 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.076432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061613 restraints weight = 20794.380| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.79 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7072 Z= 0.207 Angle : 0.723 8.027 9564 Z= 0.379 Chirality : 0.048 0.209 1046 Planarity : 0.004 0.040 1227 Dihedral : 10.056 106.431 1061 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.81 % Allowed : 19.26 % Favored : 75.93 % 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: 0.13 (0.28), residues: 870 helix: 1.54 (0.30), residues: 282 sheet: -0.75 (0.40), residues: 162 loop : -0.50 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 55 TYR 0.015 0.001 TYR A 392 PHE 0.017 0.002 PHE B 312 TRP 0.024 0.002 TRP B 364 HIS 0.008 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7072) covalent geometry : angle 0.72256 ( 9564) hydrogen bonds : bond 0.04876 ( 293) hydrogen bonds : angle 5.75428 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8764 (tpp) cc_final: 0.8527 (tpp) REVERT: A 120 ILE cc_start: 0.9077 (mt) cc_final: 0.8676 (mm) REVERT: A 174 MET cc_start: 0.8641 (ttp) cc_final: 0.8404 (ttp) REVERT: A 262 SER cc_start: 0.8575 (t) cc_final: 0.8167 (p) REVERT: A 277 MET cc_start: 0.8499 (mtt) cc_final: 0.8163 (mtt) REVERT: A 366 LYS cc_start: 0.9078 (tptp) cc_final: 0.8867 (tptp) REVERT: B 36 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: B 149 ARG cc_start: 0.8837 (tpp80) cc_final: 0.8422 (tpp-160) REVERT: B 249 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8470 (ttpp) REVERT: B 284 ARG cc_start: 0.8475 (pmt-80) cc_final: 0.8230 (pmt-80) REVERT: B 390 MET cc_start: 0.9255 (mtp) cc_final: 0.8841 (mtm) REVERT: B 444 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8438 (tpp80) REVERT: B 494 ASP cc_start: 0.7996 (m-30) cc_final: 0.7740 (t0) outliers start: 35 outliers final: 19 residues processed: 167 average time/residue: 0.0968 time to fit residues: 21.1455 Evaluate side-chains 137 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 125 ASN B 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061165 restraints weight = 20644.638| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.69 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7072 Z= 0.159 Angle : 0.621 6.814 9564 Z= 0.325 Chirality : 0.046 0.168 1046 Planarity : 0.003 0.027 1227 Dihedral : 8.671 113.662 1051 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.58 % Allowed : 21.46 % Favored : 74.97 % 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: 0.24 (0.28), residues: 870 helix: 1.79 (0.31), residues: 282 sheet: -0.54 (0.42), residues: 153 loop : -0.64 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.013 0.001 TYR A 392 PHE 0.025 0.002 PHE B 185 TRP 0.017 0.001 TRP B 376 HIS 0.014 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7072) covalent geometry : angle 0.62130 ( 9564) hydrogen bonds : bond 0.04023 ( 293) hydrogen bonds : angle 5.38528 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.8023 (mtp) cc_final: 0.7719 (mtp) REVERT: A 46 MET cc_start: 0.8759 (tpp) cc_final: 0.8502 (tpp) REVERT: A 99 MET cc_start: 0.8725 (ppp) cc_final: 0.8374 (ppp) REVERT: A 120 ILE cc_start: 0.9078 (mt) cc_final: 0.8746 (mm) REVERT: A 174 MET cc_start: 0.8557 (ttp) cc_final: 0.8244 (ttp) REVERT: A 262 SER cc_start: 0.8643 (t) cc_final: 0.8262 (p) REVERT: A 277 MET cc_start: 0.8511 (mtt) cc_final: 0.8186 (mtt) REVERT: A 325 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 366 LYS cc_start: 0.9177 (tptp) cc_final: 0.8936 (tptp) REVERT: B 36 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: B 149 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8676 (tpp80) REVERT: B 161 GLU cc_start: 0.9462 (mt-10) cc_final: 0.8753 (tt0) REVERT: B 251 PHE cc_start: 0.8159 (t80) cc_final: 0.7896 (t80) REVERT: B 284 ARG cc_start: 0.8507 (pmt-80) cc_final: 0.8248 (pmt-80) REVERT: B 364 TRP cc_start: 0.8206 (p-90) cc_final: 0.7042 (p-90) REVERT: B 384 TRP cc_start: 0.8991 (t60) cc_final: 0.8346 (t60) REVERT: B 388 LYS cc_start: 0.9669 (tptt) cc_final: 0.9361 (tppt) REVERT: B 390 MET cc_start: 0.9204 (mtp) cc_final: 0.8849 (mtm) REVERT: B 444 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8458 (tpp80) REVERT: B 445 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: B 494 ASP cc_start: 0.7990 (m-30) cc_final: 0.7717 (t0) outliers start: 26 outliers final: 14 residues processed: 147 average time/residue: 0.0913 time to fit residues: 17.5408 Evaluate side-chains 132 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 445 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059575 restraints weight = 20942.546| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.86 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7072 Z= 0.184 Angle : 0.618 11.117 9564 Z= 0.319 Chirality : 0.046 0.161 1046 Planarity : 0.003 0.026 1227 Dihedral : 8.374 119.535 1049 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.71 % Allowed : 22.70 % Favored : 73.59 % 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: 0.23 (0.28), residues: 870 helix: 1.70 (0.31), residues: 282 sheet: -0.43 (0.42), residues: 153 loop : -0.63 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 263 TYR 0.013 0.001 TYR A 392 PHE 0.026 0.002 PHE B 185 TRP 0.019 0.001 TRP B 376 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7072) covalent geometry : angle 0.61776 ( 9564) hydrogen bonds : bond 0.03751 ( 293) hydrogen bonds : angle 5.30797 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8972 (mtp) cc_final: 0.8727 (mtt) REVERT: A 99 MET cc_start: 0.8812 (ppp) cc_final: 0.8380 (ppp) REVERT: A 120 ILE cc_start: 0.9040 (mt) cc_final: 0.8749 (mm) REVERT: A 141 GLU cc_start: 0.9196 (pp20) cc_final: 0.8976 (mm-30) REVERT: A 174 MET cc_start: 0.8414 (ttp) cc_final: 0.8117 (ttp) REVERT: A 199 MET cc_start: 0.8319 (mmm) cc_final: 0.7951 (mmm) REVERT: A 262 SER cc_start: 0.8651 (t) cc_final: 0.8278 (p) REVERT: A 277 MET cc_start: 0.8416 (mtt) cc_final: 0.8103 (mtt) REVERT: A 325 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 344 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.8578 (t70) REVERT: B 36 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: B 149 ARG cc_start: 0.8954 (tpp80) cc_final: 0.8658 (tpp80) REVERT: B 182 ASN cc_start: 0.9305 (t0) cc_final: 0.9071 (t0) REVERT: B 244 ASN cc_start: 0.9386 (p0) cc_final: 0.9155 (p0) REVERT: B 251 PHE cc_start: 0.8211 (t80) cc_final: 0.7620 (t80) REVERT: B 364 TRP cc_start: 0.8278 (p-90) cc_final: 0.7061 (p-90) REVERT: B 400 ASP cc_start: 0.8624 (p0) cc_final: 0.8232 (p0) REVERT: B 401 MET cc_start: 0.8677 (ttp) cc_final: 0.8458 (ttp) REVERT: B 494 ASP cc_start: 0.7996 (m-30) cc_final: 0.7704 (t0) outliers start: 27 outliers final: 18 residues processed: 135 average time/residue: 0.0696 time to fit residues: 12.6449 Evaluate side-chains 133 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 64 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.062151 restraints weight = 20551.550| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.98 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7072 Z= 0.109 Angle : 0.590 10.691 9564 Z= 0.299 Chirality : 0.045 0.146 1046 Planarity : 0.003 0.028 1227 Dihedral : 8.032 119.916 1049 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.89 % Allowed : 25.03 % Favored : 72.08 % 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: 0.32 (0.28), residues: 870 helix: 1.77 (0.31), residues: 282 sheet: -0.45 (0.43), residues: 154 loop : -0.54 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 273 TYR 0.011 0.001 TYR A 392 PHE 0.026 0.001 PHE B 185 TRP 0.019 0.002 TRP B 376 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7072) covalent geometry : angle 0.59036 ( 9564) hydrogen bonds : bond 0.03390 ( 293) hydrogen bonds : angle 5.11865 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8755 (mt) cc_final: 0.8463 (mt) REVERT: A 66 MET cc_start: 0.8950 (mtp) cc_final: 0.8711 (mtt) REVERT: A 99 MET cc_start: 0.8907 (ppp) cc_final: 0.8486 (ppp) REVERT: A 120 ILE cc_start: 0.9018 (mt) cc_final: 0.8813 (mm) REVERT: A 141 GLU cc_start: 0.9187 (pp20) cc_final: 0.8956 (mm-30) REVERT: A 163 MET cc_start: 0.8808 (mmp) cc_final: 0.7879 (mpp) REVERT: A 262 SER cc_start: 0.8525 (t) cc_final: 0.8197 (p) REVERT: A 277 MET cc_start: 0.8401 (mtt) cc_final: 0.8171 (mtt) REVERT: A 325 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 344 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8487 (t70) REVERT: B 36 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8492 (pm20) REVERT: B 149 ARG cc_start: 0.9018 (tpp80) cc_final: 0.8729 (tpp80) REVERT: B 161 GLU cc_start: 0.9468 (mt-10) cc_final: 0.8884 (tt0) REVERT: B 178 LYS cc_start: 0.9370 (ttmm) cc_final: 0.9026 (tptp) REVERT: B 244 ASN cc_start: 0.9386 (p0) cc_final: 0.9166 (p0) REVERT: B 251 PHE cc_start: 0.8249 (t80) cc_final: 0.7658 (t80) REVERT: B 271 GLU cc_start: 0.8754 (mp0) cc_final: 0.8531 (mp0) REVERT: B 364 TRP cc_start: 0.8123 (p-90) cc_final: 0.6942 (p-90) REVERT: B 373 MET cc_start: 0.8092 (ptp) cc_final: 0.7812 (ptp) REVERT: B 400 ASP cc_start: 0.8590 (p0) cc_final: 0.8219 (p0) REVERT: B 457 MET cc_start: 0.8846 (mmt) cc_final: 0.8613 (mmm) outliers start: 21 outliers final: 15 residues processed: 141 average time/residue: 0.0794 time to fit residues: 14.9397 Evaluate side-chains 136 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061025 restraints weight = 20857.901| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 5.01 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7072 Z= 0.130 Angle : 0.581 10.136 9564 Z= 0.298 Chirality : 0.044 0.139 1046 Planarity : 0.003 0.027 1227 Dihedral : 7.847 120.856 1049 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.75 % Allowed : 25.17 % Favored : 72.08 % 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: 0.37 (0.28), residues: 870 helix: 1.76 (0.31), residues: 282 sheet: -0.39 (0.43), residues: 154 loop : -0.48 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.010 0.001 TYR A 392 PHE 0.023 0.001 PHE B 185 TRP 0.018 0.001 TRP B 376 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7072) covalent geometry : angle 0.58135 ( 9564) hydrogen bonds : bond 0.03380 ( 293) hydrogen bonds : angle 5.05084 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8123 (mtp) cc_final: 0.7899 (mtp) REVERT: A 99 MET cc_start: 0.8941 (ppp) cc_final: 0.8522 (ppp) REVERT: A 120 ILE cc_start: 0.8997 (mt) cc_final: 0.8796 (mm) REVERT: A 163 MET cc_start: 0.8820 (mmp) cc_final: 0.7952 (mpp) REVERT: A 262 SER cc_start: 0.8521 (t) cc_final: 0.8216 (p) REVERT: A 277 MET cc_start: 0.8397 (mtt) cc_final: 0.8191 (mtt) REVERT: A 285 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9208 (mmmt) REVERT: A 324 MET cc_start: 0.8458 (mmt) cc_final: 0.8078 (mtt) REVERT: A 325 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8821 (p) REVERT: A 344 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8465 (t70) REVERT: B 16 VAL cc_start: 0.9336 (t) cc_final: 0.9123 (m) REVERT: B 36 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: B 149 ARG cc_start: 0.8997 (tpp80) cc_final: 0.8704 (tpp80) REVERT: B 161 GLU cc_start: 0.9484 (mt-10) cc_final: 0.8903 (tt0) REVERT: B 178 LYS cc_start: 0.9371 (ttmm) cc_final: 0.9060 (tptp) REVERT: B 244 ASN cc_start: 0.9446 (p0) cc_final: 0.9229 (p0) REVERT: B 251 PHE cc_start: 0.8260 (t80) cc_final: 0.7662 (t80) REVERT: B 364 TRP cc_start: 0.8255 (p-90) cc_final: 0.6900 (p-90) REVERT: B 373 MET cc_start: 0.8092 (ptp) cc_final: 0.7860 (ptp) REVERT: B 390 MET cc_start: 0.9272 (mtm) cc_final: 0.8677 (mtm) REVERT: B 400 ASP cc_start: 0.8620 (p0) cc_final: 0.8251 (p0) REVERT: B 406 GLU cc_start: 0.8015 (mp0) cc_final: 0.7803 (mp0) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.0937 time to fit residues: 16.6774 Evaluate side-chains 135 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061947 restraints weight = 20552.082| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.81 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7072 Z= 0.116 Angle : 0.578 10.384 9564 Z= 0.296 Chirality : 0.044 0.145 1046 Planarity : 0.003 0.029 1227 Dihedral : 7.550 119.816 1047 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.75 % Allowed : 25.31 % Favored : 71.94 % 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: 0.46 (0.28), residues: 870 helix: 1.92 (0.31), residues: 273 sheet: -0.34 (0.42), residues: 165 loop : -0.45 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 273 TYR 0.009 0.001 TYR B 267 PHE 0.023 0.001 PHE B 185 TRP 0.019 0.001 TRP B 376 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7072) covalent geometry : angle 0.57796 ( 9564) hydrogen bonds : bond 0.03233 ( 293) hydrogen bonds : angle 5.04284 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8586 (tpp) cc_final: 0.8374 (tpp) REVERT: A 99 MET cc_start: 0.8925 (ppp) cc_final: 0.8532 (ppp) REVERT: A 163 MET cc_start: 0.8800 (mmp) cc_final: 0.7946 (mpp) REVERT: A 262 SER cc_start: 0.8532 (t) cc_final: 0.8251 (p) REVERT: A 277 MET cc_start: 0.8482 (mtt) cc_final: 0.8167 (mtp) REVERT: A 285 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9202 (mmmt) REVERT: A 325 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 344 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8436 (t70) REVERT: B 16 VAL cc_start: 0.9335 (t) cc_final: 0.9129 (m) REVERT: B 36 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: B 149 ARG cc_start: 0.9018 (tpp80) cc_final: 0.8704 (tpp80) REVERT: B 151 MET cc_start: 0.8931 (ttp) cc_final: 0.8679 (tpp) REVERT: B 161 GLU cc_start: 0.9469 (mt-10) cc_final: 0.8870 (tt0) REVERT: B 178 LYS cc_start: 0.9361 (ttmm) cc_final: 0.9094 (tptp) REVERT: B 244 ASN cc_start: 0.9426 (p0) cc_final: 0.9217 (p0) REVERT: B 251 PHE cc_start: 0.8274 (t80) cc_final: 0.7674 (t80) REVERT: B 327 LEU cc_start: 0.9313 (pp) cc_final: 0.9111 (mm) REVERT: B 373 MET cc_start: 0.8135 (ptp) cc_final: 0.7915 (ptp) REVERT: B 390 MET cc_start: 0.9240 (mtm) cc_final: 0.8982 (mtm) REVERT: B 400 ASP cc_start: 0.8615 (p0) cc_final: 0.8233 (p0) REVERT: B 433 ASP cc_start: 0.8705 (t0) cc_final: 0.8378 (t0) REVERT: B 444 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8569 (tpp80) REVERT: B 457 MET cc_start: 0.8799 (mmt) cc_final: 0.8494 (mmm) outliers start: 20 outliers final: 13 residues processed: 142 average time/residue: 0.0829 time to fit residues: 15.4028 Evaluate side-chains 135 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 373 HIS B 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058493 restraints weight = 21412.726| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.83 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7072 Z= 0.230 Angle : 0.644 9.680 9564 Z= 0.335 Chirality : 0.046 0.186 1046 Planarity : 0.003 0.032 1227 Dihedral : 7.736 123.200 1047 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.58 % Allowed : 26.55 % Favored : 69.88 % 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: 0.41 (0.28), residues: 870 helix: 1.84 (0.31), residues: 273 sheet: -0.28 (0.43), residues: 155 loop : -0.48 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.011 0.001 TYR A 392 PHE 0.021 0.002 PHE B 185 TRP 0.024 0.002 TRP B 364 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 7072) covalent geometry : angle 0.64400 ( 9564) hydrogen bonds : bond 0.03729 ( 293) hydrogen bonds : angle 5.25593 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8976 (ppp) cc_final: 0.8545 (ppp) REVERT: A 163 MET cc_start: 0.8750 (mmp) cc_final: 0.8483 (mmm) REVERT: A 221 THR cc_start: 0.9229 (p) cc_final: 0.8851 (p) REVERT: A 277 MET cc_start: 0.8543 (mtt) cc_final: 0.8220 (mtt) REVERT: A 285 LYS cc_start: 0.9404 (mmmt) cc_final: 0.9183 (mmmt) REVERT: A 324 MET cc_start: 0.8527 (mmt) cc_final: 0.8175 (mtt) REVERT: A 325 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 344 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8472 (t70) REVERT: B 16 VAL cc_start: 0.9366 (t) cc_final: 0.9147 (m) REVERT: B 149 ARG cc_start: 0.9002 (tpp80) cc_final: 0.8690 (tpp80) REVERT: B 178 LYS cc_start: 0.9335 (ttmm) cc_final: 0.9034 (tptp) REVERT: B 251 PHE cc_start: 0.8250 (t80) cc_final: 0.7638 (t80) REVERT: B 373 MET cc_start: 0.8277 (ptp) cc_final: 0.8055 (ptp) REVERT: B 400 ASP cc_start: 0.8689 (p0) cc_final: 0.8283 (p0) REVERT: B 433 ASP cc_start: 0.8839 (t0) cc_final: 0.8525 (t0) REVERT: B 445 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: B 457 MET cc_start: 0.8910 (mmt) cc_final: 0.8688 (mmm) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.0803 time to fit residues: 14.2669 Evaluate side-chains 129 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS B 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.076451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.061190 restraints weight = 20701.431| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.82 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7072 Z= 0.127 Angle : 0.652 10.633 9564 Z= 0.333 Chirality : 0.046 0.182 1046 Planarity : 0.003 0.032 1227 Dihedral : 7.498 118.891 1047 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.89 % Allowed : 27.10 % Favored : 70.01 % 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: 0.39 (0.28), residues: 870 helix: 1.88 (0.31), residues: 273 sheet: -0.31 (0.44), residues: 154 loop : -0.54 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 273 TYR 0.013 0.001 TYR B 425 PHE 0.026 0.001 PHE B 185 TRP 0.022 0.002 TRP B 376 HIS 0.008 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7072) covalent geometry : angle 0.65164 ( 9564) hydrogen bonds : bond 0.03429 ( 293) hydrogen bonds : angle 5.19936 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8559 (tpp) cc_final: 0.8334 (tpp) REVERT: A 99 MET cc_start: 0.9032 (ppp) cc_final: 0.8633 (ppp) REVERT: A 141 GLU cc_start: 0.9150 (pp20) cc_final: 0.8929 (mm-30) REVERT: A 163 MET cc_start: 0.8790 (mmp) cc_final: 0.8500 (mmm) REVERT: A 262 SER cc_start: 0.8510 (t) cc_final: 0.8155 (p) REVERT: A 277 MET cc_start: 0.8502 (mtt) cc_final: 0.7921 (mtm) REVERT: A 285 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9231 (mmmt) REVERT: A 324 MET cc_start: 0.8395 (mmt) cc_final: 0.8056 (mtt) REVERT: A 325 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 149 ARG cc_start: 0.9027 (tpp80) cc_final: 0.8740 (tpp-160) REVERT: B 161 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9040 (tt0) REVERT: B 178 LYS cc_start: 0.9358 (ttmm) cc_final: 0.9093 (tptp) REVERT: B 251 PHE cc_start: 0.8278 (t80) cc_final: 0.7673 (t80) REVERT: B 390 MET cc_start: 0.9159 (mtm) cc_final: 0.8747 (mtm) REVERT: B 400 ASP cc_start: 0.8636 (p0) cc_final: 0.8225 (p0) REVERT: B 433 ASP cc_start: 0.8789 (t0) cc_final: 0.8474 (t0) REVERT: B 457 MET cc_start: 0.8862 (mmt) cc_final: 0.8628 (mmm) outliers start: 21 outliers final: 15 residues processed: 135 average time/residue: 0.0898 time to fit residues: 16.2077 Evaluate side-chains 131 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 12 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061957 restraints weight = 20552.047| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.81 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7072 Z= 0.124 Angle : 0.649 10.472 9564 Z= 0.331 Chirality : 0.046 0.176 1046 Planarity : 0.003 0.031 1227 Dihedral : 7.350 117.137 1047 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.20 % Allowed : 27.51 % Favored : 70.29 % 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 aren not related in a simple way. whole: 0.34 (0.28), residues: 870 helix: 1.69 (0.31), residues: 284 sheet: -0.29 (0.44), residues: 154 loop : -0.53 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 273 TYR 0.014 0.001 TYR B 425 PHE 0.025 0.001 PHE B 185 TRP 0.024 0.002 TRP B 376 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7072) covalent geometry : angle 0.64907 ( 9564) hydrogen bonds : bond 0.03403 ( 293) hydrogen bonds : angle 5.16005 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8555 (tpp) cc_final: 0.8282 (tpp) REVERT: A 66 MET cc_start: 0.8550 (mtt) cc_final: 0.8345 (mtt) REVERT: A 99 MET cc_start: 0.9070 (ppp) cc_final: 0.8724 (ppp) REVERT: A 141 GLU cc_start: 0.9151 (pp20) cc_final: 0.8921 (mm-30) REVERT: A 163 MET cc_start: 0.8802 (mmp) cc_final: 0.8539 (mmm) REVERT: A 241 TYR cc_start: 0.9260 (t80) cc_final: 0.9035 (t80) REVERT: A 262 SER cc_start: 0.8501 (t) cc_final: 0.8169 (p) REVERT: A 277 MET cc_start: 0.8497 (mtt) cc_final: 0.8292 (mtt) REVERT: A 285 LYS cc_start: 0.9443 (mmmt) cc_final: 0.9239 (mmmt) REVERT: A 324 MET cc_start: 0.8370 (mmt) cc_final: 0.8045 (mtt) REVERT: A 325 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8819 (p) REVERT: B 149 ARG cc_start: 0.9187 (tpp80) cc_final: 0.8856 (tpp-160) REVERT: B 151 MET cc_start: 0.8768 (tpp) cc_final: 0.8553 (tpt) REVERT: B 161 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9032 (tt0) REVERT: B 178 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9140 (tptp) REVERT: B 251 PHE cc_start: 0.8303 (t80) cc_final: 0.7675 (t80) REVERT: B 390 MET cc_start: 0.9144 (mtm) cc_final: 0.8634 (mtm) REVERT: B 400 ASP cc_start: 0.8627 (p0) cc_final: 0.8219 (p0) REVERT: B 433 ASP cc_start: 0.8800 (t0) cc_final: 0.8483 (t0) REVERT: B 457 MET cc_start: 0.8828 (mmt) cc_final: 0.8579 (mmm) outliers start: 16 outliers final: 14 residues processed: 130 average time/residue: 0.0829 time to fit residues: 14.5731 Evaluate side-chains 131 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.061053 restraints weight = 20964.077| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.83 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7072 Z= 0.156 Angle : 0.665 10.083 9564 Z= 0.339 Chirality : 0.046 0.191 1046 Planarity : 0.003 0.033 1227 Dihedral : 7.376 117.193 1047 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.48 % Allowed : 27.10 % Favored : 70.43 % 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: 0.29 (0.28), residues: 870 helix: 1.66 (0.31), residues: 285 sheet: -0.42 (0.42), residues: 165 loop : -0.53 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 273 TYR 0.015 0.001 TYR B 425 PHE 0.023 0.002 PHE B 185 TRP 0.020 0.002 TRP B 384 HIS 0.013 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7072) covalent geometry : angle 0.66534 ( 9564) hydrogen bonds : bond 0.03516 ( 293) hydrogen bonds : angle 5.16827 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1251.53 seconds wall clock time: 22 minutes 25.38 seconds (1345.38 seconds total)