Starting phenix.real_space_refine on Fri Jul 3 02:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2026/7zrg_14913.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 7 8.98 5 P 8 5.49 5 S 62 5.16 5 C 7124 2.51 5 N 1824 2.21 5 O 2007 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: 11032 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: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5008 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 26, 'TRANS': 647} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.23 Number of scatterers: 11032 At special positions: 0 Unit cell: (100.188, 111.32, 148.764, 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 7 19.00 S 62 16.00 P 8 15.00 O 2007 8.00 N 1824 7.00 C 7124 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: 0.95 Conformation dependent library (CDL) restraints added in 470.7 milliseconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 63.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.959A pdb=" N MET A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 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 124 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.963A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.931A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.388A 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 305 removed outlier: 4.454A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.094A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.748A 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 436 removed outlier: 4.562A 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: 4.043A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.888A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 550 removed outlier: 3.991A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (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 21 removed outlier: 4.124A pdb=" N ALA C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.800A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.646A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 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 24 removed outlier: 4.748A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 61 through 97 removed outlier: 4.156A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.162A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.080A 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 264 through 285 removed outlier: 5.434A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.649A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.155A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.715A pdb=" N LYS B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.658A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 557 through 595 removed outlier: 4.123A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.570A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.751A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.488A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.082A 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: 4.044A pdb=" N GLY B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY B 661 " --> pdb=" O TYR B 657 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.602A 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: 6.336A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (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 131 through 134 removed outlier: 3.645A pdb=" N GLU B 145 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 6.549A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 307 removed outlier: 6.675A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 429 through 431 648 hydrogen bonds defined for protein. 1914 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: 1.79 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1946 1.33 - 1.45: 2647 1.45 - 1.57: 6503 1.57 - 1.70: 17 1.70 - 1.82: 112 Bond restraints: 11225 Sorted by residual: bond pdb=" OA3 CDL A 609 " pdb=" PA1 CDL A 609 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.44e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.08e+00 bond pdb=" OB3 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.08e+00 bond pdb=" C11 CDL A 608 " pdb=" C12 CDL A 608 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.50e-02 4.44e+03 4.48e+00 ... (remaining 11220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 14857 2.12 - 4.24: 295 4.24 - 6.36: 59 6.36 - 8.48: 23 8.48 - 10.59: 4 Bond angle restraints: 15238 Sorted by residual: angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.97 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C ASP B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 121.97 128.98 -7.01 1.80e+00 3.09e-01 1.52e+01 angle pdb=" CB MET B 36 " pdb=" CG MET B 36 " pdb=" SD MET B 36 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 274 " pdb=" CG MET A 274 " pdb=" SD MET A 274 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C LEU A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 120.33 123.10 -2.77 8.00e-01 1.56e+00 1.20e+01 ... (remaining 15233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5892 17.62 - 35.24: 597 35.24 - 52.86: 148 52.86 - 70.48: 37 70.48 - 88.10: 16 Dihedral angle restraints: 6690 sinusoidal: 2590 harmonic: 4100 Sorted by residual: 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 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY B 658 " pdb=" C GLY B 658 " pdb=" N LEU B 659 " pdb=" CA LEU B 659 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP B 119 " pdb=" CB ASP B 119 " pdb=" CG ASP B 119 " pdb=" OD1 ASP B 119 " ideal model delta sinusoidal sigma weight residual -30.00 -87.98 57.98 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1405 0.052 - 0.103: 337 0.103 - 0.155: 60 0.155 - 0.206: 5 0.206 - 0.258: 5 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA4 CDL A 608 " pdb=" CA3 CDL A 608 " pdb=" CA6 CDL A 608 " pdb=" OA6 CDL A 608 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 182 " pdb=" CA ILE B 182 " pdb=" CG1 ILE B 182 " pdb=" CG2 ILE B 182 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1809 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 105 " -0.016 2.00e-02 2.50e+03 2.09e-02 7.67e+00 pdb=" CG PHE B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 105 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 105 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 105 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 381 " 0.017 2.00e-02 2.50e+03 1.43e-02 4.08e+00 pdb=" CG TYR A 381 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 381 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 381 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 381 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 381 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 381 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 362 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.028 5.00e-02 4.00e+02 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 3790 2.86 - 3.43: 12485 3.43 - 4.00: 21344 4.00 - 4.57: 30580 4.57 - 5.14: 43138 Nonbonded interactions: 111337 Sorted by model distance: nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.291 3.040 nonbonded pdb=" OG SER A 325 " pdb=" O ASN C 131 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASN B 474 " pdb=" OG1 THR B 477 " model vdw 2.301 3.040 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.304 3.040 ... (remaining 111332 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11225 Z= 0.194 Angle : 0.782 10.595 15238 Z= 0.396 Chirality : 0.046 0.258 1812 Planarity : 0.005 0.049 1908 Dihedral : 16.017 88.104 4056 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1437 helix: 0.09 (0.16), residues: 881 sheet: -1.58 (0.57), residues: 87 loop : -2.02 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 107 TYR 0.035 0.002 TYR A 381 PHE 0.048 0.002 PHE B 105 TRP 0.012 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (11225) covalent geometry : angle 0.78157 / 0.40 (15238) hydrogen bonds : bond 0.08332 / 5.57 ( 648) hydrogen bonds : angle 5.02592 / 3.61 ( 1914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8029 (m-10) cc_final: 0.7828 (m-10) REVERT: B 515 MET cc_start: 0.7513 (ptm) cc_final: 0.7248 (ppp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0999 time to fit residues: 24.3905 Evaluate side-chains 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105760 restraints weight = 15133.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106361 restraints weight = 16258.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107958 restraints weight = 11588.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107613 restraints weight = 8485.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107689 restraints weight = 7736.532| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11225 Z= 0.189 Angle : 0.609 7.921 15238 Z= 0.305 Chirality : 0.041 0.162 1812 Planarity : 0.005 0.066 1908 Dihedral : 10.277 65.205 1676 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.71 % Allowed : 8.64 % Favored : 90.65 % 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: -0.30 (0.22), residues: 1437 helix: 0.89 (0.17), residues: 867 sheet: -1.71 (0.62), residues: 73 loop : -1.91 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.028 0.002 TYR A 381 PHE 0.020 0.002 PHE B 105 TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (11225) covalent geometry : angle 0.60932 / 0.30 (15238) hydrogen bonds : bond 0.04362 / 2.83 ( 648) hydrogen bonds : angle 4.30607 / 3.12 ( 1914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.422 Fit side-chains REVERT: A 135 VAL cc_start: 0.8755 (m) cc_final: 0.8508 (p) REVERT: B 125 GLN cc_start: 0.5385 (pm20) cc_final: 0.4608 (tm-30) outliers start: 8 outliers final: 5 residues processed: 156 average time/residue: 0.1046 time to fit residues: 23.7003 Evaluate side-chains 135 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.144144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107628 restraints weight = 15171.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105982 restraints weight = 13805.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107034 restraints weight = 11728.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107334 restraints weight = 8943.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107732 restraints weight = 8025.055| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11225 Z= 0.131 Angle : 0.548 8.396 15238 Z= 0.272 Chirality : 0.039 0.157 1812 Planarity : 0.004 0.038 1908 Dihedral : 9.612 64.747 1676 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.88 % Allowed : 10.67 % Favored : 88.45 % 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: 0.03 (0.22), residues: 1437 helix: 1.15 (0.17), residues: 879 sheet: -1.66 (0.63), residues: 73 loop : -1.83 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 148 TYR 0.026 0.001 TYR A 381 PHE 0.014 0.001 PHE B 105 TRP 0.006 0.001 TRP B 71 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11225) covalent geometry : angle 0.54844 / 0.27 (15238) hydrogen bonds : bond 0.03960 / 2.56 ( 648) hydrogen bonds : angle 4.15454 / 3.01 ( 1914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.416 Fit side-chains REVERT: B 13 LEU cc_start: 0.8028 (pt) cc_final: 0.7576 (pp) REVERT: B 125 GLN cc_start: 0.5373 (pm20) cc_final: 0.4810 (tm-30) REVERT: B 560 GLU cc_start: 0.7148 (pm20) cc_final: 0.6828 (mp0) outliers start: 10 outliers final: 7 residues processed: 151 average time/residue: 0.0972 time to fit residues: 21.8341 Evaluate side-chains 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 128 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 100 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.144136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108499 restraints weight = 15139.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106363 restraints weight = 15763.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107569 restraints weight = 13056.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108570 restraints weight = 9781.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108300 restraints weight = 9516.889| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11225 Z= 0.121 Angle : 0.533 9.310 15238 Z= 0.263 Chirality : 0.039 0.182 1812 Planarity : 0.004 0.043 1908 Dihedral : 9.063 63.931 1676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.59 % Allowed : 11.90 % Favored : 86.51 % 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: 0.26 (0.22), residues: 1437 helix: 1.34 (0.17), residues: 881 sheet: -1.72 (0.64), residues: 73 loop : -1.75 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 572 TYR 0.025 0.001 TYR A 381 PHE 0.013 0.001 PHE A 373 TRP 0.006 0.001 TRP B 71 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11225) covalent geometry : angle 0.53289 / 0.26 (15238) hydrogen bonds : bond 0.03821 / 2.47 ( 648) hydrogen bonds : angle 4.05845 / 2.94 ( 1914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.299 Fit side-chains REVERT: A 235 PHE cc_start: 0.8495 (t80) cc_final: 0.8238 (t80) REVERT: A 327 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: B 125 GLN cc_start: 0.5317 (pm20) cc_final: 0.4775 (tm-30) REVERT: B 560 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6779 (mp0) outliers start: 18 outliers final: 13 residues processed: 154 average time/residue: 0.0981 time to fit residues: 22.1940 Evaluate side-chains 145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 GLN ** 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 = 0.3667 r_free = 0.3667 target = 0.141349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104832 restraints weight = 15233.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103969 restraints weight = 14493.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105042 restraints weight = 13119.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105587 restraints weight = 9714.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105602 restraints weight = 8003.307| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11225 Z= 0.163 Angle : 0.567 9.083 15238 Z= 0.282 Chirality : 0.040 0.243 1812 Planarity : 0.004 0.057 1908 Dihedral : 8.898 64.140 1676 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.12 % Allowed : 13.05 % Favored : 84.83 % 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: 0.17 (0.22), residues: 1437 helix: 1.25 (0.17), residues: 877 sheet: -1.70 (0.65), residues: 73 loop : -1.73 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 572 TYR 0.026 0.001 TYR A 381 PHE 0.015 0.001 PHE A 373 TRP 0.009 0.001 TRP B 71 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (11225) covalent geometry : angle 0.56669 / 0.28 (15238) hydrogen bonds : bond 0.04153 / 2.69 ( 648) hydrogen bonds : angle 4.13355 / 2.99 ( 1914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.370 Fit side-chains REVERT: A 235 PHE cc_start: 0.8563 (t80) cc_final: 0.8357 (t80) REVERT: A 327 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: D 25 ASN cc_start: 0.7728 (m110) cc_final: 0.7481 (m110) REVERT: B 125 GLN cc_start: 0.5299 (pm20) cc_final: 0.4776 (tm-30) REVERT: B 560 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6919 (mp0) outliers start: 24 outliers final: 18 residues processed: 155 average time/residue: 0.1026 time to fit residues: 23.6046 Evaluate side-chains 144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106381 restraints weight = 15213.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105356 restraints weight = 14238.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106568 restraints weight = 12365.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107118 restraints weight = 8887.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107192 restraints weight = 7555.839| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11225 Z= 0.127 Angle : 0.535 9.802 15238 Z= 0.265 Chirality : 0.039 0.176 1812 Planarity : 0.004 0.039 1908 Dihedral : 8.541 63.624 1676 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.85 % Allowed : 14.29 % Favored : 83.86 % 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: 0.34 (0.22), residues: 1437 helix: 1.39 (0.17), residues: 876 sheet: -1.71 (0.65), residues: 73 loop : -1.63 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.025 0.001 TYR A 381 PHE 0.012 0.001 PHE A 373 TRP 0.007 0.001 TRP B 71 HIS 0.002 0.000 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11225) covalent geometry : angle 0.53521 / 0.26 (15238) hydrogen bonds : bond 0.03860 / 2.49 ( 648) hydrogen bonds : angle 4.06304 / 2.94 ( 1914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.389 Fit side-chains REVERT: A 235 PHE cc_start: 0.8535 (t80) cc_final: 0.8322 (t80) REVERT: A 327 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: C 22 TYR cc_start: 0.8752 (t80) cc_final: 0.8507 (t80) REVERT: D 25 ASN cc_start: 0.7666 (m110) cc_final: 0.7449 (m110) REVERT: B 463 MET cc_start: 0.4757 (mtt) cc_final: 0.4407 (mtm) REVERT: B 560 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6829 (mp0) outliers start: 21 outliers final: 16 residues processed: 150 average time/residue: 0.0918 time to fit residues: 20.3269 Evaluate side-chains 145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 71 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 134 optimal weight: 0.0770 chunk 67 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 80 GLN B 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109246 restraints weight = 15061.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108194 restraints weight = 10669.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109097 restraints weight = 9458.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109453 restraints weight = 7596.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109727 restraints weight = 6570.457| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11225 Z= 0.099 Angle : 0.517 9.582 15238 Z= 0.255 Chirality : 0.038 0.143 1812 Planarity : 0.003 0.037 1908 Dihedral : 7.973 62.169 1676 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.76 % Allowed : 14.73 % Favored : 83.51 % 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: 0.55 (0.23), residues: 1437 helix: 1.60 (0.18), residues: 880 sheet: -1.80 (0.61), residues: 78 loop : -1.64 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 202 TYR 0.024 0.001 TYR A 381 PHE 0.009 0.001 PHE B 105 TRP 0.008 0.001 TRP A 176 HIS 0.003 0.000 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (11225) covalent geometry : angle 0.51693 / 0.25 (15238) hydrogen bonds : bond 0.03507 / 2.26 ( 648) hydrogen bonds : angle 3.94383 / 2.85 ( 1914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 190 ILE cc_start: 0.9080 (mm) cc_final: 0.8719 (mt) REVERT: A 235 PHE cc_start: 0.8423 (t80) cc_final: 0.8209 (t80) REVERT: A 325 SER cc_start: 0.8762 (p) cc_final: 0.8534 (p) REVERT: D 25 ASN cc_start: 0.7626 (m110) cc_final: 0.7406 (m110) REVERT: B 13 LEU cc_start: 0.8044 (pt) cc_final: 0.7717 (pp) REVERT: B 125 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5418 (tm-30) REVERT: B 463 MET cc_start: 0.4830 (mtt) cc_final: 0.4488 (mtm) REVERT: B 560 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6760 (mp0) outliers start: 20 outliers final: 17 residues processed: 155 average time/residue: 0.0946 time to fit residues: 21.6114 Evaluate side-chains 153 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 127 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.141714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106127 restraints weight = 15125.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104804 restraints weight = 15676.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105889 restraints weight = 13512.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106617 restraints weight = 10262.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106430 restraints weight = 9825.580| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11225 Z= 0.144 Angle : 0.556 8.096 15238 Z= 0.275 Chirality : 0.040 0.153 1812 Planarity : 0.004 0.049 1908 Dihedral : 8.018 62.425 1676 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.03 % Allowed : 15.52 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1437 helix: 1.55 (0.17), residues: 874 sheet: -1.70 (0.65), residues: 73 loop : -1.64 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.025 0.001 TYR A 381 PHE 0.014 0.001 PHE A 373 TRP 0.008 0.001 TRP B 71 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (11225) covalent geometry : angle 0.55610 / 0.27 (15238) hydrogen bonds : bond 0.03872 / 2.50 ( 648) hydrogen bonds : angle 4.01124 / 2.91 ( 1914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.352 Fit side-chains REVERT: A 235 PHE cc_start: 0.8573 (t80) cc_final: 0.8365 (t80) REVERT: A 325 SER cc_start: 0.8836 (p) cc_final: 0.8630 (p) REVERT: A 327 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: A 471 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.5978 (m-10) REVERT: D 25 ASN cc_start: 0.7642 (m110) cc_final: 0.7429 (m110) REVERT: B 463 MET cc_start: 0.5142 (mtt) cc_final: 0.4794 (mtm) outliers start: 23 outliers final: 19 residues processed: 147 average time/residue: 0.0912 time to fit residues: 20.0240 Evaluate side-chains 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 119 optimal weight: 30.0000 chunk 3 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107032 restraints weight = 14997.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106282 restraints weight = 10494.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106476 restraints weight = 9766.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106617 restraints weight = 8349.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107314 restraints weight = 7609.860| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11225 Z= 0.109 Angle : 0.533 7.214 15238 Z= 0.264 Chirality : 0.039 0.148 1812 Planarity : 0.003 0.037 1908 Dihedral : 7.757 62.104 1676 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.94 % Allowed : 15.70 % Favored : 82.36 % 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: 0.55 (0.22), residues: 1437 helix: 1.61 (0.18), residues: 874 sheet: -1.86 (0.60), residues: 78 loop : -1.59 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.024 0.001 TYR A 381 PHE 0.011 0.001 PHE B 105 TRP 0.008 0.001 TRP A 176 HIS 0.003 0.000 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11225) covalent geometry : angle 0.53277 / 0.26 (15238) hydrogen bonds : bond 0.03637 / 2.34 ( 648) hydrogen bonds : angle 3.94800 / 2.86 ( 1914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 325 SER cc_start: 0.8762 (p) cc_final: 0.8561 (p) REVERT: A 327 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: A 489 MET cc_start: 0.8501 (mtm) cc_final: 0.8292 (mtt) REVERT: B 13 LEU cc_start: 0.8099 (pt) cc_final: 0.7839 (pp) REVERT: B 125 GLN cc_start: 0.5643 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: B 463 MET cc_start: 0.5046 (mtt) cc_final: 0.4748 (mtm) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.0970 time to fit residues: 21.3710 Evaluate side-chains 147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 139 optimal weight: 0.0570 chunk 86 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106978 restraints weight = 15091.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105969 restraints weight = 14696.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106810 restraints weight = 12329.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107101 restraints weight = 10170.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107504 restraints weight = 8498.719| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11225 Z= 0.119 Angle : 0.549 9.939 15238 Z= 0.269 Chirality : 0.039 0.148 1812 Planarity : 0.003 0.037 1908 Dihedral : 7.703 61.994 1676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.85 % Allowed : 15.78 % Favored : 82.36 % 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: 1437 helix: 1.60 (0.18), residues: 874 sheet: -1.88 (0.60), residues: 78 loop : -1.59 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.024 0.001 TYR A 381 PHE 0.012 0.001 PHE A 373 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11225) covalent geometry : angle 0.54898 / 0.27 (15238) hydrogen bonds : bond 0.03672 / 2.37 ( 648) hydrogen bonds : angle 3.95804 / 2.87 ( 1914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.617 Fit side-chains REVERT: A 325 SER cc_start: 0.8763 (p) cc_final: 0.8562 (p) REVERT: A 327 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: A 489 MET cc_start: 0.8671 (mtm) cc_final: 0.8455 (mtt) REVERT: B 13 LEU cc_start: 0.8035 (pt) cc_final: 0.7784 (pp) REVERT: B 463 MET cc_start: 0.5086 (mtt) cc_final: 0.4811 (mtm) outliers start: 21 outliers final: 18 residues processed: 144 average time/residue: 0.0885 time to fit residues: 19.2565 Evaluate side-chains 147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105176 restraints weight = 15096.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104366 restraints weight = 14886.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105376 restraints weight = 13189.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105884 restraints weight = 9786.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106028 restraints weight = 8285.710| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11225 Z= 0.144 Angle : 0.563 7.724 15238 Z= 0.278 Chirality : 0.040 0.158 1812 Planarity : 0.004 0.042 1908 Dihedral : 7.852 62.549 1676 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.03 % Allowed : 15.96 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1437 helix: 1.51 (0.17), residues: 868 sheet: -1.82 (0.61), residues: 78 loop : -1.58 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.024 0.002 TYR A 381 PHE 0.013 0.001 PHE A 373 TRP 0.006 0.001 TRP A 59 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (11225) covalent geometry : angle 0.56259 / 0.28 (15238) hydrogen bonds : bond 0.03899 / 2.52 ( 648) hydrogen bonds : angle 4.03067 / 2.92 ( 1914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.22 seconds wall clock time: 31 minutes 9.26 seconds (1869.26 seconds total)