Starting phenix.real_space_refine on Wed Mar 4 06:35:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zre_14912/03_2026/7zre_14912.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zre_14912/03_2026/7zre_14912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zre_14912/03_2026/7zre_14912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zre_14912/03_2026/7zre_14912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zre_14912/03_2026/7zre_14912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zre_14912/03_2026/7zre_14912.map" } resolution = 3.4 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 101 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 9 8.98 5 P 6 5.49 5 S 62 5.16 5 C 7105 2.51 5 N 1818 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10996 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5001 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 26, 'TRANS': 646} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.23, per 1000 atoms: 0.20 Number of scatterers: 10996 At special positions: 0 Unit cell: (89.056, 112.332, 143.704, 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) K 9 19.00 S 62 16.00 P 6 15.00 O 1996 8.00 N 1818 7.00 C 7105 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: 0.81 Conformation dependent library (CDL) restraints added in 536.0 milliseconds 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 63.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.788A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.361A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.558A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 304 removed outlier: 4.566A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.401A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.787A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.365A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.028A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 550 removed outlier: 4.209A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 34 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 133 through 149 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.550A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 23 removed outlier: 4.272A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 63 through 103 removed outlier: 3.751A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 246 removed outlier: 4.048A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.761A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 265 through 284 removed outlier: 5.522A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.939A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 556 through 582 removed outlier: 3.995A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.654A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.458A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.327A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.572A pdb=" N LYS A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.409A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 120 removed outlier: 3.720A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.522A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 288 removed outlier: 6.411A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP B 518 " --> pdb=" O PHD B 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.957A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET B 383 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 377 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1771 1.31 - 1.44: 2725 1.44 - 1.57: 6563 1.57 - 1.69: 13 1.69 - 1.82: 112 Bond restraints: 11184 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.592 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.424 -0.090 1.10e-02 8.26e+03 6.76e+01 bond pdb=" CB7 CDL A 608 " pdb=" OB8 CDL A 608 " ideal model delta sigma weight residual 1.334 1.422 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CA7 CDL A 608 " pdb=" OA8 CDL A 608 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.43e+01 bond pdb=" CA7 CDL A 609 " pdb=" OA8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.414 -0.080 1.10e-02 8.26e+03 5.28e+01 ... (remaining 11179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 14672 2.24 - 4.47: 354 4.47 - 6.71: 119 6.71 - 8.95: 25 8.95 - 11.18: 7 Bond angle restraints: 15177 Sorted by residual: angle pdb=" C51 CDL A 609 " pdb=" CB5 CDL A 609 " pdb=" OB6 CDL A 609 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL A 608 " pdb=" CA5 CDL A 608 " pdb=" OA6 CDL A 608 " ideal model delta sigma weight residual 111.33 120.12 -8.79 1.32e+00 5.72e-01 4.42e+01 angle pdb=" C11 CDL A 609 " pdb=" CA5 CDL A 609 " pdb=" OA6 CDL A 609 " ideal model delta sigma weight residual 111.33 119.83 -8.50 1.32e+00 5.72e-01 4.14e+01 angle pdb=" C51 CDL A 608 " pdb=" CB5 CDL A 608 " pdb=" OB6 CDL A 608 " ideal model delta sigma weight residual 111.33 119.63 -8.30 1.32e+00 5.72e-01 3.94e+01 angle pdb=" C71 CDL A 609 " pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 111.64 120.47 -8.83 1.65e+00 3.69e-01 2.88e+01 ... (remaining 15172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5890 17.92 - 35.85: 624 35.85 - 53.77: 152 53.77 - 71.70: 44 71.70 - 89.62: 12 Dihedral angle restraints: 6722 sinusoidal: 2625 harmonic: 4097 Sorted by residual: dihedral pdb=" C PHD B 307 " pdb=" N PHD B 307 " pdb=" CA PHD B 307 " pdb=" CB PHD B 307 " ideal model delta harmonic sigma weight residual -122.60 -137.22 14.62 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" N PHD B 307 " pdb=" C PHD B 307 " pdb=" CA PHD B 307 " pdb=" CB PHD B 307 " ideal model delta harmonic sigma weight residual 122.80 134.98 -12.18 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 6719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1729 0.104 - 0.207: 73 0.207 - 0.311: 4 0.311 - 0.414: 0 0.414 - 0.518: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA PHD B 307 " pdb=" N PHD B 307 " pdb=" C PHD B 307 " pdb=" CB PHD B 307 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA LEU B 342 " pdb=" N LEU B 342 " pdb=" C LEU B 342 " pdb=" CB LEU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE B 393 " pdb=" CA ILE B 393 " pdb=" CG1 ILE B 393 " pdb=" CG2 ILE B 393 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1804 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A 362 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 360 " 0.011 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE B 360 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 360 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 360 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 360 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 360 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 360 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 18 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C THR C 18 " -0.037 2.00e-02 2.50e+03 pdb=" O THR C 18 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 2986 2.81 - 3.39: 12509 3.39 - 3.98: 21778 3.98 - 4.56: 30403 4.56 - 5.14: 44182 Nonbonded interactions: 111858 Sorted by model distance: nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" O CYS A 344 " model vdw 2.248 3.040 nonbonded pdb=" O TYR C 22 " pdb=" OG1 THR C 26 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 612 " pdb=" OD1 ASP B 614 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 241 " pdb=" O ILE A 348 " model vdw 2.278 3.040 ... (remaining 111853 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 11184 Z= 0.354 Angle : 0.929 11.183 15177 Z= 0.471 Chirality : 0.049 0.518 1807 Planarity : 0.006 0.080 1905 Dihedral : 16.337 89.620 4090 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.08 % 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: -0.86 (0.20), residues: 1433 helix: 0.17 (0.16), residues: 884 sheet: -1.05 (0.58), residues: 82 loop : -1.79 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 504 TYR 0.030 0.002 TYR B 114 PHE 0.037 0.002 PHE B 360 TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00610 (11184) covalent geometry : angle 0.92889 (15177) hydrogen bonds : bond 0.11329 ( 690) hydrogen bonds : angle 5.99018 ( 2031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8414 (mt) cc_final: 0.8142 (mt) REVERT: A 365 LEU cc_start: 0.7753 (tp) cc_final: 0.7524 (tp) REVERT: B 186 TRP cc_start: 0.6306 (p-90) cc_final: 0.5586 (p-90) REVERT: B 279 MET cc_start: 0.7084 (mmm) cc_final: 0.6817 (mtm) REVERT: B 393 ILE cc_start: 0.6839 (mm) cc_final: 0.6596 (mm) REVERT: B 515 MET cc_start: 0.6470 (tmm) cc_final: 0.5536 (tmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0956 time to fit residues: 22.3087 Evaluate side-chains 134 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 39 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096110 restraints weight = 14973.936| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.41 r_work: 0.2946 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11184 Z= 0.277 Angle : 0.726 10.932 15177 Z= 0.368 Chirality : 0.047 0.193 1807 Planarity : 0.005 0.067 1905 Dihedral : 11.252 65.836 1714 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.33 % Allowed : 9.98 % Favored : 88.69 % 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: -0.43 (0.21), residues: 1433 helix: 0.56 (0.17), residues: 881 sheet: -1.41 (0.52), residues: 97 loop : -1.60 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 382 TYR 0.037 0.003 TYR A 381 PHE 0.021 0.002 PHE A 471 TRP 0.014 0.002 TRP B 655 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00655 (11184) covalent geometry : angle 0.72593 (15177) hydrogen bonds : bond 0.05155 ( 690) hydrogen bonds : angle 5.31666 ( 2031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.391 Fit side-chains REVERT: A 27 LEU cc_start: 0.8518 (mt) cc_final: 0.8257 (mt) REVERT: A 43 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: C 32 TRP cc_start: 0.8120 (t60) cc_final: 0.7891 (t60) REVERT: B 186 TRP cc_start: 0.6515 (p-90) cc_final: 0.5482 (p-90) REVERT: B 279 MET cc_start: 0.8105 (mmm) cc_final: 0.7705 (mmt) REVERT: B 469 MET cc_start: 0.8127 (ppp) cc_final: 0.7783 (ptt) REVERT: B 515 MET cc_start: 0.7367 (tmm) cc_final: 0.7089 (tmm) outliers start: 15 outliers final: 9 residues processed: 149 average time/residue: 0.0849 time to fit residues: 19.2567 Evaluate side-chains 145 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107029 restraints weight = 14627.795| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.37 r_work: 0.3042 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11184 Z= 0.120 Angle : 0.548 8.160 15177 Z= 0.279 Chirality : 0.040 0.159 1807 Planarity : 0.004 0.053 1905 Dihedral : 10.471 59.345 1714 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.15 % Allowed : 12.90 % Favored : 85.95 % 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: 0.18 (0.21), residues: 1433 helix: 1.15 (0.17), residues: 873 sheet: -1.31 (0.51), residues: 97 loop : -1.52 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 5 TYR 0.027 0.001 TYR A 381 PHE 0.011 0.001 PHE A 260 TRP 0.007 0.001 TRP B 71 HIS 0.001 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00259 (11184) covalent geometry : angle 0.54833 (15177) hydrogen bonds : bond 0.03968 ( 690) hydrogen bonds : angle 4.94915 ( 2031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.383 Fit side-chains REVERT: A 27 LEU cc_start: 0.8522 (mt) cc_final: 0.8227 (mt) REVERT: C 141 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8499 (mp) REVERT: D 25 ASN cc_start: 0.6368 (m-40) cc_final: 0.6099 (m110) REVERT: B 133 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6708 (pp) REVERT: B 186 TRP cc_start: 0.6611 (p-90) cc_final: 0.5663 (p-90) REVERT: B 279 MET cc_start: 0.8053 (mmm) cc_final: 0.7635 (mmt) REVERT: B 471 THR cc_start: 0.7062 (m) cc_final: 0.6786 (p) REVERT: B 515 MET cc_start: 0.7406 (tmm) cc_final: 0.6956 (tmm) outliers start: 13 outliers final: 5 residues processed: 154 average time/residue: 0.0854 time to fit residues: 20.0365 Evaluate side-chains 139 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 69 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107131 restraints weight = 14560.319| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.33 r_work: 0.3071 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11184 Z= 0.121 Angle : 0.533 7.744 15177 Z= 0.271 Chirality : 0.040 0.168 1807 Planarity : 0.004 0.049 1905 Dihedral : 9.983 58.593 1714 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.41 % Allowed : 13.07 % Favored : 85.51 % 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: 0.41 (0.22), residues: 1433 helix: 1.36 (0.17), residues: 875 sheet: -1.29 (0.53), residues: 93 loop : -1.48 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.025 0.001 TYR A 381 PHE 0.011 0.001 PHE B 578 TRP 0.009 0.001 TRP C 32 HIS 0.001 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00263 (11184) covalent geometry : angle 0.53328 (15177) hydrogen bonds : bond 0.03857 ( 690) hydrogen bonds : angle 4.79118 ( 2031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.401 Fit side-chains REVERT: A 27 LEU cc_start: 0.8507 (mt) cc_final: 0.8226 (mt) REVERT: C 141 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 25 ASN cc_start: 0.6342 (m-40) cc_final: 0.6075 (m110) REVERT: B 133 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6704 (pp) REVERT: B 186 TRP cc_start: 0.6539 (p-90) cc_final: 0.5536 (p-90) REVERT: B 279 MET cc_start: 0.7816 (mmm) cc_final: 0.7423 (mmt) REVERT: B 393 ILE cc_start: 0.6870 (mm) cc_final: 0.6654 (mm) REVERT: B 515 MET cc_start: 0.7533 (tmm) cc_final: 0.7046 (tmm) outliers start: 16 outliers final: 7 residues processed: 153 average time/residue: 0.0848 time to fit residues: 19.8587 Evaluate side-chains 144 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 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 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107160 restraints weight = 14604.845| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.32 r_work: 0.3068 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11184 Z= 0.119 Angle : 0.531 9.285 15177 Z= 0.268 Chirality : 0.040 0.155 1807 Planarity : 0.004 0.043 1905 Dihedral : 9.717 59.990 1714 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.94 % Allowed : 13.96 % Favored : 84.10 % 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: 0.54 (0.22), residues: 1433 helix: 1.46 (0.17), residues: 874 sheet: -1.25 (0.54), residues: 93 loop : -1.42 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.026 0.002 TYR A 381 PHE 0.011 0.001 PHE B 360 TRP 0.007 0.001 TRP C 32 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00260 (11184) covalent geometry : angle 0.53130 (15177) hydrogen bonds : bond 0.03798 ( 690) hydrogen bonds : angle 4.72683 ( 2031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.499 Fit side-chains REVERT: A 27 LEU cc_start: 0.8505 (mt) cc_final: 0.8221 (mt) REVERT: C 1 MET cc_start: 0.5168 (mtm) cc_final: 0.4565 (mtt) REVERT: C 141 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8538 (mp) REVERT: C 170 TYR cc_start: 0.7654 (p90) cc_final: 0.7401 (p90) REVERT: D 25 ASN cc_start: 0.6390 (m-40) cc_final: 0.6121 (m110) REVERT: B 51 ILE cc_start: 0.8054 (mm) cc_final: 0.7727 (mm) REVERT: B 133 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6679 (pp) REVERT: B 186 TRP cc_start: 0.6468 (p-90) cc_final: 0.5442 (p-90) REVERT: B 279 MET cc_start: 0.7840 (mmm) cc_final: 0.7463 (mmt) REVERT: B 393 ILE cc_start: 0.6815 (mm) cc_final: 0.6579 (mm) REVERT: B 515 MET cc_start: 0.7526 (tmm) cc_final: 0.7029 (tmm) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 0.0880 time to fit residues: 20.2036 Evaluate side-chains 147 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN B 80 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098903 restraints weight = 14970.213| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.38 r_work: 0.2990 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11184 Z= 0.127 Angle : 0.539 9.444 15177 Z= 0.271 Chirality : 0.040 0.157 1807 Planarity : 0.004 0.042 1905 Dihedral : 9.580 59.088 1714 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.03 % Allowed : 14.93 % Favored : 83.04 % 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: 0.58 (0.22), residues: 1433 helix: 1.49 (0.17), residues: 872 sheet: -1.28 (0.51), residues: 99 loop : -1.37 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.025 0.002 TYR A 381 PHE 0.014 0.001 PHE B 360 TRP 0.010 0.001 TRP C 32 HIS 0.001 0.000 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00282 (11184) covalent geometry : angle 0.53900 (15177) hydrogen bonds : bond 0.03845 ( 690) hydrogen bonds : angle 4.70262 ( 2031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.398 Fit side-chains REVERT: A 27 LEU cc_start: 0.8502 (mt) cc_final: 0.8224 (mt) REVERT: A 43 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: C 1 MET cc_start: 0.5182 (mtm) cc_final: 0.4606 (mtt) REVERT: C 128 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 141 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 170 TYR cc_start: 0.7693 (p90) cc_final: 0.7428 (p90) REVERT: D 25 ASN cc_start: 0.6410 (m-40) cc_final: 0.6176 (m110) REVERT: B 51 ILE cc_start: 0.8100 (mm) cc_final: 0.7771 (mm) REVERT: B 133 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6587 (pp) REVERT: B 186 TRP cc_start: 0.6489 (p-90) cc_final: 0.5462 (p-90) REVERT: B 279 MET cc_start: 0.7872 (mmm) cc_final: 0.7480 (mmt) REVERT: B 393 ILE cc_start: 0.6819 (mm) cc_final: 0.6603 (mm) REVERT: B 504 ARG cc_start: 0.7411 (mmt90) cc_final: 0.7041 (mmm160) REVERT: B 515 MET cc_start: 0.7526 (tmm) cc_final: 0.7044 (tmm) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.0900 time to fit residues: 20.4760 Evaluate side-chains 150 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 0.0050 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN B 80 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.100477 restraints weight = 14778.005| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.37 r_work: 0.2980 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11184 Z= 0.183 Angle : 0.595 9.508 15177 Z= 0.299 Chirality : 0.042 0.172 1807 Planarity : 0.004 0.042 1905 Dihedral : 9.799 59.891 1714 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.47 % Allowed : 15.90 % Favored : 81.63 % 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: 0.35 (0.22), residues: 1433 helix: 1.28 (0.17), residues: 877 sheet: -1.37 (0.51), residues: 99 loop : -1.43 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.026 0.002 TYR A 381 PHE 0.015 0.001 PHE B 360 TRP 0.007 0.001 TRP C 32 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00428 (11184) covalent geometry : angle 0.59489 (15177) hydrogen bonds : bond 0.04338 ( 690) hydrogen bonds : angle 4.86720 ( 2031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.384 Fit side-chains REVERT: A 27 LEU cc_start: 0.8526 (mt) cc_final: 0.8249 (mt) REVERT: A 43 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6121 (mt-10) REVERT: C 128 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 141 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8550 (mp) REVERT: D 25 ASN cc_start: 0.6650 (m-40) cc_final: 0.6400 (m110) REVERT: B 87 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 133 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6583 (pp) REVERT: B 186 TRP cc_start: 0.6482 (p-90) cc_final: 0.5471 (p-90) REVERT: B 279 MET cc_start: 0.7917 (mmm) cc_final: 0.7531 (mmt) outliers start: 28 outliers final: 18 residues processed: 155 average time/residue: 0.0886 time to fit residues: 20.7139 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104016 restraints weight = 14704.441| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.38 r_work: 0.3030 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11184 Z= 0.112 Angle : 0.540 9.084 15177 Z= 0.271 Chirality : 0.040 0.161 1807 Planarity : 0.004 0.040 1905 Dihedral : 9.411 59.643 1714 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.50 % Allowed : 17.23 % Favored : 81.27 % 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: 0.63 (0.22), residues: 1433 helix: 1.53 (0.17), residues: 872 sheet: -1.26 (0.55), residues: 82 loop : -1.36 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.024 0.001 TYR A 381 PHE 0.017 0.001 PHE B 360 TRP 0.012 0.001 TRP C 32 HIS 0.001 0.000 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00239 (11184) covalent geometry : angle 0.53954 (15177) hydrogen bonds : bond 0.03693 ( 690) hydrogen bonds : angle 4.70242 ( 2031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.416 Fit side-chains REVERT: A 27 LEU cc_start: 0.8505 (mt) cc_final: 0.8232 (mt) REVERT: A 114 ASN cc_start: 0.8881 (m-40) cc_final: 0.8659 (m-40) REVERT: A 363 MET cc_start: 0.8456 (ttm) cc_final: 0.8219 (ttm) REVERT: C 128 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8434 (mt) REVERT: C 141 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8524 (mp) REVERT: D 25 ASN cc_start: 0.6408 (m-40) cc_final: 0.6192 (m110) REVERT: B 51 ILE cc_start: 0.8118 (mm) cc_final: 0.7793 (mm) REVERT: B 186 TRP cc_start: 0.6511 (p-90) cc_final: 0.5549 (p-90) REVERT: B 504 ARG cc_start: 0.7420 (mmt90) cc_final: 0.6972 (mmm160) REVERT: B 515 MET cc_start: 0.7585 (tmm) cc_final: 0.7195 (tmm) REVERT: B 629 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8282 (t) outliers start: 17 outliers final: 8 residues processed: 155 average time/residue: 0.0894 time to fit residues: 20.8673 Evaluate side-chains 146 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 88 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102426 restraints weight = 14611.712| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.36 r_work: 0.3040 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11184 Z= 0.132 Angle : 0.563 8.778 15177 Z= 0.281 Chirality : 0.041 0.157 1807 Planarity : 0.004 0.041 1905 Dihedral : 9.360 59.314 1714 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.50 % Allowed : 17.40 % Favored : 81.10 % 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: 0.62 (0.22), residues: 1433 helix: 1.52 (0.17), residues: 872 sheet: -1.38 (0.50), residues: 99 loop : -1.31 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.025 0.002 TYR A 381 PHE 0.018 0.001 PHE B 360 TRP 0.014 0.001 TRP C 32 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00296 (11184) covalent geometry : angle 0.56303 (15177) hydrogen bonds : bond 0.03859 ( 690) hydrogen bonds : angle 4.70646 ( 2031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.330 Fit side-chains REVERT: A 27 LEU cc_start: 0.8518 (mt) cc_final: 0.8244 (mt) REVERT: A 114 ASN cc_start: 0.8896 (m-40) cc_final: 0.8677 (m-40) REVERT: C 128 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8451 (mt) REVERT: C 141 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8536 (mp) REVERT: D 25 ASN cc_start: 0.6509 (m-40) cc_final: 0.6261 (m110) REVERT: B 51 ILE cc_start: 0.8126 (mm) cc_final: 0.7794 (mm) REVERT: B 133 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6697 (pp) REVERT: B 186 TRP cc_start: 0.6514 (p-90) cc_final: 0.5580 (p-90) REVERT: B 279 MET cc_start: 0.7918 (mmm) cc_final: 0.7641 (mmm) REVERT: B 504 ARG cc_start: 0.7440 (mmt90) cc_final: 0.7035 (mmm160) REVERT: B 515 MET cc_start: 0.7582 (tmm) cc_final: 0.7179 (tmm) REVERT: B 530 ASP cc_start: 0.5715 (m-30) cc_final: 0.5380 (m-30) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 0.0839 time to fit residues: 18.9850 Evaluate side-chains 146 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 134 optimal weight: 0.0470 overall best weight: 1.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102646 restraints weight = 14766.275| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.37 r_work: 0.3038 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11184 Z= 0.137 Angle : 0.579 14.300 15177 Z= 0.286 Chirality : 0.041 0.211 1807 Planarity : 0.004 0.041 1905 Dihedral : 9.343 59.691 1714 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.77 % Allowed : 17.58 % Favored : 80.65 % 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: 0.60 (0.22), residues: 1433 helix: 1.48 (0.17), residues: 878 sheet: -1.26 (0.55), residues: 82 loop : -1.36 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.024 0.001 TYR A 381 PHE 0.016 0.001 PHE A 270 TRP 0.013 0.001 TRP C 33 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00308 (11184) covalent geometry : angle 0.57877 (15177) hydrogen bonds : bond 0.03884 ( 690) hydrogen bonds : angle 4.71126 ( 2031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.380 Fit side-chains REVERT: A 27 LEU cc_start: 0.8519 (mt) cc_final: 0.8244 (mt) REVERT: A 114 ASN cc_start: 0.8901 (m-40) cc_final: 0.8689 (m-40) REVERT: C 128 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8419 (mt) REVERT: C 141 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8554 (mp) REVERT: D 25 ASN cc_start: 0.6520 (m-40) cc_final: 0.6280 (m110) REVERT: B 51 ILE cc_start: 0.8133 (mm) cc_final: 0.7794 (mm) REVERT: B 133 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6624 (pp) REVERT: B 186 TRP cc_start: 0.6479 (p-90) cc_final: 0.5548 (p-90) REVERT: B 279 MET cc_start: 0.7950 (mmm) cc_final: 0.7673 (mmm) REVERT: B 504 ARG cc_start: 0.7440 (mmt90) cc_final: 0.7045 (mmm160) REVERT: B 515 MET cc_start: 0.7600 (tmm) cc_final: 0.7233 (tmm) REVERT: B 530 ASP cc_start: 0.5717 (m-30) cc_final: 0.5385 (m-30) outliers start: 20 outliers final: 16 residues processed: 153 average time/residue: 0.0816 time to fit residues: 19.0517 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101997 restraints weight = 14709.403| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.37 r_work: 0.3031 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11184 Z= 0.140 Angle : 0.579 12.086 15177 Z= 0.287 Chirality : 0.042 0.171 1807 Planarity : 0.004 0.041 1905 Dihedral : 9.327 59.989 1714 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.94 % Allowed : 17.58 % Favored : 80.48 % 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: 0.60 (0.22), residues: 1433 helix: 1.48 (0.17), residues: 878 sheet: -1.24 (0.55), residues: 82 loop : -1.35 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.024 0.001 TYR A 381 PHE 0.019 0.001 PHE B 360 TRP 0.013 0.001 TRP C 33 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00316 (11184) covalent geometry : angle 0.57931 (15177) hydrogen bonds : bond 0.03922 ( 690) hydrogen bonds : angle 4.71322 ( 2031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.37 seconds wall clock time: 43 minutes 40.77 seconds (2620.77 seconds total)