Starting phenix.real_space_refine on Fri Jul 3 02:11:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zre_14912/07_2026/7zre_14912.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zre_14912/07_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_14912/07_2026/7zre_14912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zre_14912/07_2026/7zre_14912.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zre_14912/07_2026/7zre_14912.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zre_14912/07_2026/7zre_14912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zre_14912/07_2026/7zre_14912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zre_14912/07_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-6108/lib/python3.11/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: 2.12, per 1000 atoms: 0.19 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: 0.82 Conformation dependent library (CDL) restraints added in 415.7 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: 0.22 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: 1.72 Time building geometry restraints manager: 1.02 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: 5878 17.92 - 35.85: 612 35.85 - 53.77: 144 53.77 - 71.70: 37 71.70 - 89.62: 11 Dihedral angle restraints: 6682 sinusoidal: 2585 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 6679 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.260 Find NCS groups from input model: 0.030 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 15.965 89.620 4050 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/Z covalent geometry : bond 0.00610 / 0.35 (11184) covalent geometry : angle 0.92889 / 0.47 (15177) hydrogen bonds : bond 0.11329 / 7.62 ( 690) hydrogen bonds : angle 5.99018 / 4.33 ( 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 : 0.255 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: 0.0777 time to fit residues: 18.1053 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 : 0.294 ------------------------------------------------------------------------------- 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... ** 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 = 0.3590 r_free = 0.3590 target = 0.135274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.099437 restraints weight = 14834.400| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.38 r_work: 0.2990 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 11184 Z= 0.277 Angle : 0.713 10.698 15177 Z= 0.363 Chirality : 0.047 0.185 1807 Planarity : 0.005 0.067 1905 Dihedral : 9.930 59.930 1674 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.41 % Allowed : 9.89 % 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: -0.40 (0.21), residues: 1433 helix: 0.58 (0.17), residues: 881 sheet: -1.33 (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 0.022 0.002 PHE A 471 TRP 0.013 0.002 TRP B 655 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.28 (11184) covalent geometry : angle 0.71316 / 0.36 (15177) hydrogen bonds : bond 0.05056 / 3.51 ( 690) hydrogen bonds : angle 5.30123 / 3.84 ( 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: 16 poor density : 142 time to evaluate : 0.368 Fit side-chains REVERT: A 27 LEU cc_start: 0.8516 (mt) cc_final: 0.8254 (mt) REVERT: A 43 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6717 (mt-10) REVERT: B 186 TRP cc_start: 0.6549 (p-90) cc_final: 0.5538 (p-90) REVERT: B 279 MET cc_start: 0.8078 (mmm) cc_final: 0.7669 (mmt) REVERT: B 469 MET cc_start: 0.8096 (ppp) cc_final: 0.7874 (ptt) REVERT: B 515 MET cc_start: 0.7371 (tmm) cc_final: 0.7063 (tmm) outliers start: 16 outliers final: 10 residues processed: 149 average time/residue: 0.0817 time to fit residues: 18.5853 Evaluate side-chains 145 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 168 GLU 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: 1.9990 chunk 98 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 44 optimal weight: 0.0670 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN 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 = 0.3670 r_free = 0.3670 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106639 restraints weight = 14645.340| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.34 r_work: 0.3065 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1571 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= 0.116 Angle : 0.544 8.357 15177 Z= 0.276 Chirality : 0.040 0.157 1807 Planarity : 0.004 0.053 1905 Dihedral : 9.073 59.953 1674 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.24 % Allowed : 12.54 % Favored : 86.22 % 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: 0.21 (0.21), residues: 1433 helix: 1.19 (0.17), residues: 873 sheet: -1.29 (0.51), residues: 97 loop : -1.54 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.000 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (11184) covalent geometry : angle 0.54351 / 0.28 (15177) hydrogen bonds : bond 0.03924 / 2.71 ( 690) hydrogen bonds : angle 4.92437 / 3.57 ( 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 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.403 Fit side-chains REVERT: A 27 LEU cc_start: 0.8525 (mt) cc_final: 0.8237 (mt) REVERT: C 141 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 133 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6699 (pp) REVERT: B 186 TRP cc_start: 0.6628 (p-90) cc_final: 0.5673 (p-90) REVERT: B 279 MET cc_start: 0.8028 (mmm) cc_final: 0.7621 (mmt) REVERT: B 469 MET cc_start: 0.7966 (ppp) cc_final: 0.7734 (ptt) REVERT: B 471 THR cc_start: 0.7065 (m) cc_final: 0.6770 (p) REVERT: B 513 VAL cc_start: 0.8324 (t) cc_final: 0.8104 (t) REVERT: B 515 MET cc_start: 0.7364 (tmm) cc_final: 0.6900 (tmm) outliers start: 14 outliers final: 5 residues processed: 156 average time/residue: 0.0835 time to fit residues: 19.9355 Evaluate side-chains 141 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 246 ASN 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 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: 0.8980 chunk 75 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN C 39 ASN B 80 ASN B 563 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109616 restraints weight = 14497.804| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.32 r_work: 0.3119 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11184 Z= 0.106 Angle : 0.518 7.611 15177 Z= 0.263 Chirality : 0.040 0.185 1807 Planarity : 0.004 0.046 1905 Dihedral : 8.365 58.515 1674 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.50 % Allowed : 12.90 % Favored : 85.60 % 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: 1.52 (0.17), residues: 874 sheet: -1.19 (0.53), residues: 93 loop : -1.43 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.027 0.001 TYR A 381 PHE 0.011 0.001 PHE B 360 TRP 0.009 0.001 TRP C 32 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (11184) covalent geometry : angle 0.51816 / 0.26 (15177) hydrogen bonds : bond 0.03604 / 2.48 ( 690) hydrogen bonds : angle 4.68679 / 3.40 ( 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 165 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.366 Fit side-chains REVERT: A 27 LEU cc_start: 0.8494 (mt) cc_final: 0.8202 (mt) REVERT: C 1 MET cc_start: 0.5078 (mtm) cc_final: 0.4520 (mtt) REVERT: C 141 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 170 TYR cc_start: 0.7790 (p90) cc_final: 0.7539 (p90) REVERT: B 87 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7430 (mt-10) REVERT: B 133 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6699 (pp) REVERT: B 186 TRP cc_start: 0.6507 (p-90) cc_final: 0.5517 (p-90) REVERT: B 187 LEU cc_start: 0.7162 (tp) cc_final: 0.6955 (tp) REVERT: B 279 MET cc_start: 0.7830 (mmm) cc_final: 0.7452 (mmt) REVERT: B 393 ILE cc_start: 0.6858 (mm) cc_final: 0.6637 (mm) REVERT: B 504 ARG cc_start: 0.7421 (mmt90) cc_final: 0.7014 (mmm160) REVERT: B 515 MET cc_start: 0.7461 (tmm) cc_final: 0.7002 (tmm) REVERT: B 629 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8188 (t) outliers start: 17 outliers final: 7 residues processed: 157 average time/residue: 0.0744 time to fit residues: 17.8594 Evaluate side-chains 149 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 141 ILE 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: 6.9990 chunk 94 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 112 optimal weight: 0.0060 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 overall best weight: 0.7556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 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 = 0.3684 r_free = 0.3684 target = 0.142734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107585 restraints weight = 14622.222| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.38 r_work: 0.3090 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11184 Z= 0.112 Angle : 0.521 9.022 15177 Z= 0.262 Chirality : 0.040 0.148 1807 Planarity : 0.004 0.040 1905 Dihedral : 8.120 58.991 1674 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.50 % Allowed : 14.05 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.22), residues: 1433 helix: 1.60 (0.17), residues: 874 sheet: -1.19 (0.51), residues: 99 loop : -1.36 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.026 0.001 TYR A 381 PHE 0.011 0.001 PHE B 360 TRP 0.006 0.001 TRP B 71 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11184) covalent geometry : angle 0.52081 / 0.26 (15177) hydrogen bonds : bond 0.03652 / 2.52 ( 690) hydrogen bonds : angle 4.62298 / 3.35 ( 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: 17 poor density : 143 time to evaluate : 0.419 Fit side-chains REVERT: A 27 LEU cc_start: 0.8486 (mt) cc_final: 0.8193 (mt) REVERT: C 1 MET cc_start: 0.5119 (mtm) cc_final: 0.4531 (mtt) REVERT: C 141 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8541 (mp) REVERT: C 170 TYR cc_start: 0.7702 (p90) cc_final: 0.7428 (p90) REVERT: B 51 ILE cc_start: 0.8087 (mm) cc_final: 0.7787 (mm) REVERT: B 133 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6661 (pp) REVERT: B 186 TRP cc_start: 0.6522 (p-90) cc_final: 0.5465 (p-90) REVERT: B 187 LEU cc_start: 0.7139 (tp) cc_final: 0.6929 (tp) REVERT: B 279 MET cc_start: 0.7820 (mmm) cc_final: 0.7440 (mmt) REVERT: B 393 ILE cc_start: 0.6802 (mm) cc_final: 0.6571 (mm) REVERT: B 471 THR cc_start: 0.7187 (m) cc_final: 0.6973 (p) REVERT: B 504 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7034 (mmm160) REVERT: B 515 MET cc_start: 0.7462 (tmm) cc_final: 0.6979 (tmm) outliers start: 17 outliers final: 8 residues processed: 154 average time/residue: 0.0766 time to fit residues: 18.0454 Evaluate side-chains 151 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 320 MET 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 465 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 93 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3570 r_free = 0.3570 target = 0.133106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097118 restraints weight = 15053.435| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.38 r_work: 0.2957 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11184 Z= 0.160 Angle : 0.572 9.116 15177 Z= 0.288 Chirality : 0.042 0.162 1807 Planarity : 0.004 0.042 1905 Dihedral : 8.251 58.667 1674 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.94 % Allowed : 15.02 % 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: 0.57 (0.22), residues: 1433 helix: 1.47 (0.17), residues: 874 sheet: -1.30 (0.50), residues: 99 loop : -1.37 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 148 TYR 0.027 0.002 TYR A 381 PHE 0.014 0.001 PHE B 360 TRP 0.008 0.001 TRP C 32 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (11184) covalent geometry : angle 0.57227 / 0.29 (15177) hydrogen bonds : bond 0.04129 / 2.86 ( 690) hydrogen bonds : angle 4.74994 / 3.43 ( 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 162 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.388 Fit side-chains REVERT: A 27 LEU cc_start: 0.8507 (mt) cc_final: 0.8223 (mt) REVERT: C 1 MET cc_start: 0.5160 (mtm) cc_final: 0.4542 (mtt) REVERT: C 128 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8346 (mt) REVERT: C 141 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8559 (mp) REVERT: D 25 ASN cc_start: 0.6524 (m-40) cc_final: 0.6317 (m110) REVERT: B 133 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6578 (pp) REVERT: B 186 TRP cc_start: 0.6491 (p-90) cc_final: 0.5438 (p-90) REVERT: B 187 LEU cc_start: 0.7272 (tp) cc_final: 0.7054 (tp) REVERT: B 279 MET cc_start: 0.7860 (mmm) cc_final: 0.7487 (mmt) REVERT: B 393 ILE cc_start: 0.6833 (mm) cc_final: 0.6622 (mm) outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 0.0809 time to fit residues: 18.8266 Evaluate side-chains 151 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 320 MET 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 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 465 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3637 r_free = 0.3637 target = 0.139169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103921 restraints weight = 14660.808| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.38 r_work: 0.3049 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11184 Z= 0.123 Angle : 0.540 8.923 15177 Z= 0.272 Chirality : 0.040 0.156 1807 Planarity : 0.004 0.040 1905 Dihedral : 8.038 58.888 1674 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.59 % Allowed : 16.34 % Favored : 82.07 % 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: 0.66 (0.22), residues: 1433 helix: 1.56 (0.17), residues: 872 sheet: -1.27 (0.50), residues: 99 loop : -1.33 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.025 0.001 TYR A 381 PHE 0.015 0.001 PHE B 360 TRP 0.011 0.001 TRP C 32 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11184) covalent geometry : angle 0.54011 / 0.27 (15177) hydrogen bonds : bond 0.03804 / 2.62 ( 690) hydrogen bonds : angle 4.66813 / 3.37 ( 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 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.268 Fit side-chains REVERT: A 27 LEU cc_start: 0.8503 (mt) cc_final: 0.8215 (mt) REVERT: C 5 ARG cc_start: 0.7402 (tpt-90) cc_final: 0.6945 (tpt170) REVERT: C 141 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 25 ASN cc_start: 0.6404 (m-40) cc_final: 0.6200 (m110) REVERT: B 51 ILE cc_start: 0.8107 (mm) cc_final: 0.7774 (mm) REVERT: B 133 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6518 (pp) REVERT: B 186 TRP cc_start: 0.6480 (p-90) cc_final: 0.5497 (p-90) REVERT: B 187 LEU cc_start: 0.7230 (tp) cc_final: 0.6961 (tp) REVERT: B 393 ILE cc_start: 0.6778 (mm) cc_final: 0.6572 (mm) REVERT: B 504 ARG cc_start: 0.7419 (mmt90) cc_final: 0.7051 (mmm160) REVERT: B 515 MET cc_start: 0.7614 (tmm) cc_final: 0.7216 (tmm) outliers start: 18 outliers final: 10 residues processed: 153 average time/residue: 0.0788 time to fit residues: 18.0934 Evaluate side-chains 147 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 387 VAL Chi-restraints excluded: chain A residue 497 ILE 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 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: 7.9990 chunk 139 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109009 restraints weight = 14526.686| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.32 r_work: 0.3122 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11184 Z= 0.106 Angle : 0.529 10.013 15177 Z= 0.263 Chirality : 0.039 0.152 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.644 58.991 1674 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.50 % Allowed : 16.70 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1433 helix: 1.70 (0.18), residues: 871 sheet: -1.20 (0.54), residues: 84 loop : -1.27 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.025 0.001 TYR A 381 PHE 0.020 0.001 PHE B 360 TRP 0.015 0.001 TRP C 32 HIS 0.001 0.000 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (11184) covalent geometry : angle 0.52876 / 0.26 (15177) hydrogen bonds : bond 0.03518 / 2.41 ( 690) hydrogen bonds : angle 4.54829 / 3.28 ( 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 : 0.398 Fit side-chains REVERT: A 27 LEU cc_start: 0.8491 (mt) cc_final: 0.8201 (mt) REVERT: A 114 ASN cc_start: 0.8864 (m-40) cc_final: 0.8647 (m-40) REVERT: C 141 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8577 (mp) REVERT: D 25 ASN cc_start: 0.6182 (m-40) cc_final: 0.5927 (m110) REVERT: B 51 ILE cc_start: 0.8086 (mm) cc_final: 0.7779 (mm) REVERT: B 186 TRP cc_start: 0.6520 (p-90) cc_final: 0.5534 (p-90) REVERT: B 187 LEU cc_start: 0.7144 (tp) cc_final: 0.6873 (tp) REVERT: B 279 MET cc_start: 0.7882 (mmm) cc_final: 0.7607 (mmm) REVERT: B 393 ILE cc_start: 0.6746 (mm) cc_final: 0.6521 (mm) REVERT: B 504 ARG cc_start: 0.7404 (mmt90) cc_final: 0.7055 (mmm160) REVERT: B 515 MET cc_start: 0.7665 (tmm) cc_final: 0.7240 (tmm) REVERT: B 629 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (t) outliers start: 17 outliers final: 11 residues processed: 154 average time/residue: 0.0853 time to fit residues: 20.0711 Evaluate side-chains 150 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET 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 12 ILE 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 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: 6.9990 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 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 = 0.3632 r_free = 0.3632 target = 0.138598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103457 restraints weight = 14612.105| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.37 r_work: 0.3066 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11184 Z= 0.121 Angle : 0.550 13.182 15177 Z= 0.272 Chirality : 0.040 0.212 1807 Planarity : 0.004 0.041 1905 Dihedral : 7.631 58.867 1674 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.33 % Allowed : 17.76 % Favored : 80.92 % 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: 0.80 (0.22), residues: 1433 helix: 1.65 (0.17), residues: 872 sheet: -1.28 (0.50), residues: 101 loop : -1.22 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.026 0.001 TYR A 381 PHE 0.019 0.001 PHE B 360 TRP 0.014 0.001 TRP C 32 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11184) covalent geometry : angle 0.55022 / 0.27 (15177) hydrogen bonds : bond 0.03673 / 2.53 ( 690) hydrogen bonds : angle 4.55884 / 3.29 ( 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 152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.452 Fit side-chains REVERT: A 27 LEU cc_start: 0.8497 (mt) cc_final: 0.8215 (mt) REVERT: A 114 ASN cc_start: 0.8892 (m-40) cc_final: 0.8664 (m-40) REVERT: C 141 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8596 (mp) REVERT: D 25 ASN cc_start: 0.6326 (m-40) cc_final: 0.6121 (m110) REVERT: B 51 ILE cc_start: 0.8106 (mm) cc_final: 0.7784 (mm) REVERT: B 133 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6592 (pp) REVERT: B 186 TRP cc_start: 0.6496 (p-90) cc_final: 0.5534 (p-90) REVERT: B 187 LEU cc_start: 0.7162 (tp) cc_final: 0.6889 (tp) REVERT: B 279 MET cc_start: 0.7914 (mmm) cc_final: 0.7634 (mmm) REVERT: B 504 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7036 (mmm160) REVERT: B 515 MET cc_start: 0.7648 (tmm) cc_final: 0.7217 (tmm) outliers start: 15 outliers final: 12 residues processed: 148 average time/residue: 0.0879 time to fit residues: 20.0740 Evaluate side-chains 150 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 A residue 497 ILE Chi-restraints excluded: chain A residue 508 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 chunk 134 optimal weight: 0.0870 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 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 = 0.3687 r_free = 0.3687 target = 0.143191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108203 restraints weight = 14563.153| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.37 r_work: 0.3112 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11184 Z= 0.107 Angle : 0.539 11.634 15177 Z= 0.267 Chirality : 0.040 0.190 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.478 56.633 1674 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.41 % Allowed : 17.76 % Favored : 80.83 % 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: 0.89 (0.22), residues: 1433 helix: 1.75 (0.17), residues: 866 sheet: -1.31 (0.52), residues: 90 loop : -1.18 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.024 0.001 TYR A 381 PHE 0.020 0.001 PHE B 360 TRP 0.012 0.001 TRP C 32 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11184) covalent geometry : angle 0.53858 / 0.27 (15177) hydrogen bonds : bond 0.03503 / 2.40 ( 690) hydrogen bonds : angle 4.50865 / 3.25 ( 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 156 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.330 Fit side-chains REVERT: A 27 LEU cc_start: 0.8495 (mt) cc_final: 0.8203 (mt) REVERT: A 114 ASN cc_start: 0.8879 (m-40) cc_final: 0.8655 (m-40) REVERT: A 366 MET cc_start: 0.8602 (ttp) cc_final: 0.8364 (ttp) REVERT: C 141 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 51 ILE cc_start: 0.8082 (mm) cc_final: 0.7766 (mm) REVERT: B 186 TRP cc_start: 0.6522 (p-90) cc_final: 0.5608 (p-90) REVERT: B 187 LEU cc_start: 0.7165 (tp) cc_final: 0.6897 (tp) REVERT: B 279 MET cc_start: 0.7888 (mmm) cc_final: 0.7611 (mmm) REVERT: B 504 ARG cc_start: 0.7404 (mmt90) cc_final: 0.7044 (mmm160) REVERT: B 515 MET cc_start: 0.7641 (tmm) cc_final: 0.7215 (tmm) REVERT: B 629 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8261 (t) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.0848 time to fit residues: 19.3354 Evaluate side-chains 150 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 347 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 12 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 58 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109794 restraints weight = 14423.120| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.31 r_work: 0.3136 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1894 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= 0.107 Angle : 0.542 11.086 15177 Z= 0.268 Chirality : 0.040 0.204 1807 Planarity : 0.003 0.040 1905 Dihedral : 7.353 55.677 1674 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.77 % Allowed : 17.40 % Favored : 80.83 % 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: 0.95 (0.22), residues: 1433 helix: 1.79 (0.17), residues: 863 sheet: -1.09 (0.54), residues: 84 loop : -1.20 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.024 0.001 TYR A 381 PHE 0.010 0.001 PHE B 578 TRP 0.012 0.001 TRP C 32 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (11184) covalent geometry : angle 0.54248 / 0.27 (15177) hydrogen bonds : bond 0.03495 / 2.40 ( 690) hydrogen bonds : angle 4.48215 / 3.23 ( 2031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.33 seconds wall clock time: 42 minutes 33.75 seconds (2553.75 seconds total)