Starting phenix.real_space_refine on Fri Jul 3 02:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrk_14917/07_2026/7zrk_14917.map" } resolution = 3.1 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 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 12 8.98 5 P 8 5.49 5 S 62 5.16 5 C 7133 2.51 5 N 1826 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 11050 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: 5025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5025 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} 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: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 211 Unusual residues: {' K': 11, 'CDL': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.22, per 1000 atoms: 0.20 Number of scatterers: 11050 At special positions: 0 Unit cell: (98.164, 116.38, 146.74, 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 12 19.00 S 62 16.00 P 8 15.00 O 2009 8.00 N 1826 7.00 C 7133 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: 0.84 Conformation dependent library (CDL) restraints added in 491.6 milliseconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 64.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.860A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 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 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.734A 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 177 through 193 removed outlier: 3.913A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.835A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.509A 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: 4.290A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 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: 4.503A 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 Processing helix chain 'A' and resid 478 through 509 removed outlier: 4.691A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 4.386A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 550 removed outlier: 4.074A 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 21 removed outlier: 3.764A 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 40 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.997A pdb=" N SER C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.661A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.732A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) 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 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.656A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 99 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 247 removed outlier: 4.011A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.692A 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: 5.819A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.989A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.834A pdb=" N LYS B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 426 removed outlier: 4.171A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.799A pdb=" N LYS B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.549A 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 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 595 removed outlier: 4.017A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.971A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.337A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.114A 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: 4.244A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (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 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.845A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.638A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.837A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.791A pdb=" N SER B 152 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 5.597A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 535 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY B 472 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.768A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 396 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1980 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: 1.40 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1785 1.32 - 1.45: 2749 1.45 - 1.57: 6576 1.57 - 1.70: 16 1.70 - 1.82: 112 Bond restraints: 11238 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.606 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C ILE C 141 " pdb=" N PRO C 142 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.36e-02 5.41e+03 1.21e+01 bond pdb=" C51 CDL A 613 " pdb=" C52 CDL A 613 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.50e-02 4.44e+03 8.66e+00 bond pdb=" OB3 CDL A 613 " pdb=" PB2 CDL A 613 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.34e+00 bond pdb=" OA3 CDL A 612 " pdb=" PA1 CDL A 612 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.15e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14776 1.88 - 3.77: 360 3.77 - 5.65: 82 5.65 - 7.53: 32 7.53 - 9.41: 6 Bond angle restraints: 15256 Sorted by residual: angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 112.96 107.91 5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 121.13 -7.23 1.80e+00 3.09e-01 1.61e+01 angle pdb=" C MET B 392 " pdb=" N ILE B 393 " pdb=" CA ILE B 393 " ideal model delta sigma weight residual 120.69 126.14 -5.45 1.46e+00 4.69e-01 1.40e+01 angle pdb=" C ARG B 391 " pdb=" N MET B 392 " pdb=" CA MET B 392 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C LEU A 380 " pdb=" N TYR A 381 " pdb=" CA TYR A 381 " ideal model delta sigma weight residual 121.14 115.60 5.54 1.75e+00 3.27e-01 1.00e+01 ... (remaining 15251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 6246 24.80 - 49.59: 400 49.59 - 74.39: 50 74.39 - 99.19: 9 99.19 - 123.98: 1 Dihedral angle restraints: 6706 sinusoidal: 2600 harmonic: 4106 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 63.98 -123.98 1 2.00e+01 2.50e-03 3.74e+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 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA THR B 471 " pdb=" C THR B 471 " pdb=" N GLY B 472 " pdb=" CA GLY B 472 " ideal model delta harmonic sigma weight residual 180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1394 0.051 - 0.101: 337 0.101 - 0.152: 70 0.152 - 0.203: 10 0.203 - 0.253: 4 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB4 CDL A 613 " pdb=" CB3 CDL A 613 " pdb=" CB6 CDL A 613 " pdb=" OB6 CDL A 613 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA4 CDL A 612 " pdb=" CA3 CDL A 612 " pdb=" CA6 CDL A 612 " pdb=" OA6 CDL A 612 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA4 CDL A 613 " pdb=" CA3 CDL A 613 " pdb=" CA6 CDL A 613 " pdb=" OA6 CDL A 613 " both_signs ideal model delta sigma weight residual False -2.57 -2.35 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1812 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 163 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 164 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 496 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 58 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO B 59 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.033 5.00e-02 4.00e+02 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3302 2.83 - 3.41: 12547 3.41 - 3.98: 22053 3.98 - 4.56: 31145 4.56 - 5.14: 44819 Nonbonded interactions: 113866 Sorted by model distance: nonbonded pdb=" OE2 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 149 " pdb=" OG SER B 169 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR B 47 " pdb=" OG SER B 69 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 615 " pdb=" OD1 ASP B 673 " model vdw 2.322 3.040 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.324 3.040 ... (remaining 113861 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.870 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.005 0.210 11238 Z= 0.231 Angle : 0.773 9.415 15256 Z= 0.390 Chirality : 0.047 0.253 1815 Planarity : 0.006 0.084 1910 Dihedral : 15.745 123.983 4068 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -0.25 (0.21), residues: 1436 helix: 0.67 (0.16), residues: 854 sheet: -0.82 (0.78), residues: 49 loop : -1.43 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 48 TYR 0.021 0.002 TYR A 381 PHE 0.021 0.002 PHE B 9 TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (11238) covalent geometry : angle 0.77345 / 0.39 (15256) hydrogen bonds : bond 0.09223 / 6.04 ( 674) hydrogen bonds : angle 5.18855 / 3.87 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.300 Fit side-chains REVERT: A 6 PHE cc_start: 0.7967 (t80) cc_final: 0.7690 (t80) REVERT: A 414 MET cc_start: 0.7693 (mmm) cc_final: 0.7469 (mmp) REVERT: B 609 CYS cc_start: 0.7899 (m) cc_final: 0.7645 (m) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0851 time to fit residues: 20.0931 Evaluate side-chains 134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105060 restraints weight = 13068.472| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.45 r_work: 0.2992 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11238 Z= 0.128 Angle : 0.547 6.548 15256 Z= 0.273 Chirality : 0.039 0.164 1815 Planarity : 0.004 0.056 1910 Dihedral : 10.696 111.608 1688 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.35 % Allowed : 6.26 % Favored : 93.39 % 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: 1436 helix: 1.47 (0.18), residues: 867 sheet: -1.21 (0.68), residues: 57 loop : -1.40 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.030 0.001 TYR A 381 PHE 0.020 0.001 PHE B 377 TRP 0.015 0.001 TRP B 31 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11238) covalent geometry : angle 0.54670 / 0.27 (15256) hydrogen bonds : bond 0.04087 / 2.71 ( 674) hydrogen bonds : angle 4.39277 / 3.20 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.343 Fit side-chains REVERT: A 6 PHE cc_start: 0.8298 (t80) cc_final: 0.7935 (t80) REVERT: A 211 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7571 (mm-40) REVERT: A 408 LYS cc_start: 0.8387 (mptt) cc_final: 0.8109 (mptt) REVERT: A 445 MET cc_start: 0.8627 (mtt) cc_final: 0.8293 (mtt) REVERT: C 48 THR cc_start: 0.8324 (t) cc_final: 0.7910 (m) REVERT: C 93 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7516 (tp30) REVERT: B 318 GLN cc_start: 0.6307 (pt0) cc_final: 0.5764 (mt0) outliers start: 4 outliers final: 4 residues processed: 140 average time/residue: 0.0886 time to fit residues: 18.6960 Evaluate side-chains 135 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.099355 restraints weight = 13342.593| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.47 r_work: 0.2955 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11238 Z= 0.126 Angle : 0.532 7.158 15256 Z= 0.263 Chirality : 0.039 0.167 1815 Planarity : 0.004 0.048 1910 Dihedral : 10.073 107.933 1688 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.53 % Allowed : 9.61 % Favored : 89.86 % 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: 0.89 (0.22), residues: 1436 helix: 1.76 (0.18), residues: 869 sheet: -1.27 (0.66), residues: 57 loop : -1.27 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.028 0.001 TYR A 381 PHE 0.014 0.001 PHE B 377 TRP 0.008 0.001 TRP B 71 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (11238) covalent geometry : angle 0.53166 / 0.26 (15256) hydrogen bonds : bond 0.04023 / 2.67 ( 674) hydrogen bonds : angle 4.27300 / 3.08 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.356 Fit side-chains REVERT: A 6 PHE cc_start: 0.8321 (t80) cc_final: 0.7996 (t80) REVERT: A 211 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7546 (mm-40) REVERT: A 408 LYS cc_start: 0.8429 (mptt) cc_final: 0.8021 (mptt) REVERT: C 93 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7527 (tp30) REVERT: B 58 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.4639 (tpt) REVERT: B 318 GLN cc_start: 0.6187 (pt0) cc_final: 0.5680 (mt0) outliers start: 6 outliers final: 4 residues processed: 146 average time/residue: 0.0872 time to fit residues: 19.0752 Evaluate side-chains 140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 25 ASN ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101060 restraints weight = 13364.212| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.79 r_work: 0.2918 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11238 Z= 0.138 Angle : 0.535 6.034 15256 Z= 0.267 Chirality : 0.040 0.171 1815 Planarity : 0.004 0.047 1910 Dihedral : 9.860 107.295 1688 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.97 % Allowed : 11.20 % Favored : 87.83 % 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: 0.98 (0.22), residues: 1436 helix: 1.82 (0.18), residues: 869 sheet: -1.20 (0.66), residues: 55 loop : -1.21 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.027 0.001 TYR A 381 PHE 0.013 0.001 PHE A 109 TRP 0.008 0.001 TRP B 245 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11238) covalent geometry : angle 0.53549 / 0.27 (15256) hydrogen bonds : bond 0.04098 / 2.72 ( 674) hydrogen bonds : angle 4.26945 / 3.06 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.386 Fit side-chains REVERT: A 6 PHE cc_start: 0.8378 (t80) cc_final: 0.8062 (t80) REVERT: B 58 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.4687 (tpt) REVERT: B 111 GLU cc_start: 0.2268 (pm20) cc_final: 0.1842 (tt0) REVERT: B 318 GLN cc_start: 0.6253 (pt0) cc_final: 0.5826 (pp30) outliers start: 11 outliers final: 7 residues processed: 140 average time/residue: 0.0864 time to fit residues: 18.4400 Evaluate side-chains 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 110 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN B 30 GLN B 528 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096324 restraints weight = 13343.220| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.76 r_work: 0.2827 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11238 Z= 0.185 Angle : 0.583 7.336 15256 Z= 0.290 Chirality : 0.042 0.180 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.928 108.677 1688 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.15 % Allowed : 12.52 % Favored : 86.33 % 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: 1436 helix: 1.69 (0.18), residues: 867 sheet: -0.81 (0.62), residues: 67 loop : -1.28 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.025 0.002 TYR A 381 PHE 0.015 0.002 PHE A 494 TRP 0.006 0.001 TRP B 245 HIS 0.005 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (11238) covalent geometry : angle 0.58321 / 0.29 (15256) hydrogen bonds : bond 0.04551 / 3.03 ( 674) hydrogen bonds : angle 4.41924 / 3.16 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.396 Fit side-chains REVERT: A 544 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8228 (mm) REVERT: C 93 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7351 (tp30) REVERT: B 58 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.4957 (tpt) REVERT: B 111 GLU cc_start: 0.2311 (pm20) cc_final: 0.1897 (tt0) REVERT: B 318 GLN cc_start: 0.6318 (pt0) cc_final: 0.5864 (pp30) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 0.0840 time to fit residues: 17.5518 Evaluate side-chains 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102050 restraints weight = 13120.914| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.45 r_work: 0.2923 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 0.038 11238 Z= 0.119 Angle : 0.530 8.482 15256 Z= 0.263 Chirality : 0.039 0.169 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.569 105.819 1688 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.23 % Allowed : 13.49 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1436 helix: 1.90 (0.18), residues: 869 sheet: -0.81 (0.62), residues: 67 loop : -1.20 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.026 0.001 TYR A 381 PHE 0.011 0.001 PHE A 373 TRP 0.008 0.001 TRP B 245 HIS 0.002 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11238) covalent geometry : angle 0.52956 / 0.26 (15256) hydrogen bonds : bond 0.04002 / 2.66 ( 674) hydrogen bonds : angle 4.26515 / 3.05 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.403 Fit side-chains REVERT: A 6 PHE cc_start: 0.8395 (t80) cc_final: 0.8098 (t80) REVERT: A 544 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8237 (mm) REVERT: C 93 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7449 (tp30) REVERT: B 58 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5049 (tpp) REVERT: B 111 GLU cc_start: 0.2108 (pm20) cc_final: 0.1718 (tt0) REVERT: B 318 GLN cc_start: 0.6321 (pt0) cc_final: 0.5878 (pp30) REVERT: B 467 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7946 (t) outliers start: 14 outliers final: 6 residues processed: 142 average time/residue: 0.0928 time to fit residues: 19.7932 Evaluate side-chains 138 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.099183 restraints weight = 13193.592| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.68 r_work: 0.2881 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11238 Z= 0.137 Angle : 0.548 8.795 15256 Z= 0.270 Chirality : 0.040 0.170 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.485 106.316 1688 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.32 % Allowed : 13.67 % Favored : 85.01 % 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: 1.08 (0.22), residues: 1436 helix: 1.88 (0.18), residues: 875 sheet: -0.75 (0.62), residues: 67 loop : -1.22 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.026 0.001 TYR A 381 PHE 0.013 0.001 PHE A 373 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11238) covalent geometry : angle 0.54794 / 0.27 (15256) hydrogen bonds : bond 0.04122 / 2.74 ( 674) hydrogen bonds : angle 4.29166 / 3.07 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.472 Fit side-chains REVERT: A 6 PHE cc_start: 0.8363 (t80) cc_final: 0.8080 (t80) REVERT: A 544 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8256 (mm) REVERT: C 93 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 58 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.4992 (tpp) REVERT: B 111 GLU cc_start: 0.2243 (pm20) cc_final: 0.1855 (tt0) REVERT: B 318 GLN cc_start: 0.6334 (pt0) cc_final: 0.5871 (pp30) outliers start: 15 outliers final: 9 residues processed: 142 average time/residue: 0.0933 time to fit residues: 20.0068 Evaluate side-chains 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 29 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100354 restraints weight = 13248.806| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.99 r_work: 0.2853 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11238 Z= 0.143 Angle : 0.554 9.780 15256 Z= 0.273 Chirality : 0.040 0.172 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.443 106.324 1688 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.06 % Allowed : 14.20 % Favored : 84.74 % 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: 1.07 (0.22), residues: 1436 helix: 1.86 (0.17), residues: 875 sheet: -0.70 (0.65), residues: 62 loop : -1.22 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.026 0.001 TYR A 381 PHE 0.013 0.001 PHE A 373 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11238) covalent geometry : angle 0.55408 / 0.27 (15256) hydrogen bonds : bond 0.04173 / 2.77 ( 674) hydrogen bonds : angle 4.31158 / 3.08 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.390 Fit side-chains REVERT: A 544 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8224 (mm) REVERT: C 93 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7341 (tp30) REVERT: B 58 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5086 (tpp) REVERT: B 111 GLU cc_start: 0.2354 (pm20) cc_final: 0.1926 (tt0) REVERT: B 318 GLN cc_start: 0.6303 (pt0) cc_final: 0.5825 (pp30) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.0944 time to fit residues: 19.8843 Evaluate side-chains 144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 139 optimal weight: 0.0170 chunk 116 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105827 restraints weight = 12988.020| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.86 r_work: 0.2946 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11238 Z= 0.108 Angle : 0.529 10.357 15256 Z= 0.259 Chirality : 0.039 0.160 1815 Planarity : 0.004 0.047 1910 Dihedral : 9.233 103.701 1688 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.88 % Allowed : 14.46 % Favored : 84.66 % 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: 1.25 (0.23), residues: 1436 helix: 2.04 (0.18), residues: 874 sheet: -0.81 (0.66), residues: 63 loop : -1.17 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.025 0.001 TYR A 381 PHE 0.011 0.001 PHE A 494 TRP 0.007 0.001 TRP B 71 HIS 0.002 0.000 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11238) covalent geometry : angle 0.52890 / 0.26 (15256) hydrogen bonds : bond 0.03787 / 2.51 ( 674) hydrogen bonds : angle 4.20448 / 3.02 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 6 PHE cc_start: 0.8280 (t80) cc_final: 0.7968 (t80) REVERT: A 544 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8258 (mm) REVERT: C 93 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7416 (tp30) REVERT: B 58 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.4937 (tpp) REVERT: B 111 GLU cc_start: 0.2212 (pm20) cc_final: 0.1889 (tt0) REVERT: B 318 GLN cc_start: 0.6327 (pt0) cc_final: 0.5875 (pp30) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.0999 time to fit residues: 20.4915 Evaluate side-chains 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 93 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 0.0010 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110518 restraints weight = 13094.820| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.90 r_work: 0.2999 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11238 Z= 0.098 Angle : 0.512 10.779 15256 Z= 0.251 Chirality : 0.038 0.145 1815 Planarity : 0.004 0.048 1910 Dihedral : 8.853 101.040 1688 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.62 % Allowed : 14.73 % Favored : 84.66 % 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: 1.45 (0.23), residues: 1436 helix: 2.14 (0.17), residues: 881 sheet: -0.66 (0.67), residues: 63 loop : -1.06 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.026 0.001 TYR A 381 PHE 0.012 0.001 PHE A 494 TRP 0.008 0.001 TRP C 36 HIS 0.002 0.000 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (11238) covalent geometry : angle 0.51221 / 0.25 (15256) hydrogen bonds : bond 0.03536 / 2.33 ( 674) hydrogen bonds : angle 4.07082 / 2.94 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.411 Fit side-chains REVERT: A 6 PHE cc_start: 0.8187 (t80) cc_final: 0.7892 (t80) REVERT: A 408 LYS cc_start: 0.8465 (mptt) cc_final: 0.8052 (mmtp) REVERT: A 544 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8253 (mm) REVERT: C 93 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7507 (tp30) REVERT: B 58 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.4843 (tpp) REVERT: B 111 GLU cc_start: 0.2184 (pm20) cc_final: 0.1921 (tt0) REVERT: B 318 GLN cc_start: 0.6325 (pt0) cc_final: 0.5819 (pp30) REVERT: B 392 MET cc_start: 0.5140 (ptt) cc_final: 0.4583 (ppp) REVERT: B 568 MET cc_start: 0.8409 (mtp) cc_final: 0.8197 (mtm) outliers start: 7 outliers final: 5 residues processed: 144 average time/residue: 0.0926 time to fit residues: 20.1714 Evaluate side-chains 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 149 ASN D 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101012 restraints weight = 13178.258| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.76 r_work: 0.2948 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11238 Z= 0.145 Angle : 0.552 10.870 15256 Z= 0.273 Chirality : 0.040 0.161 1815 Planarity : 0.004 0.047 1910 Dihedral : 9.026 103.660 1688 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.71 % Allowed : 14.81 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1436 helix: 1.99 (0.17), residues: 881 sheet: -0.59 (0.66), residues: 64 loop : -1.05 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.027 0.002 TYR A 381 PHE 0.014 0.001 PHE A 373 TRP 0.007 0.001 TRP B 71 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (11238) covalent geometry : angle 0.55205 / 0.27 (15256) hydrogen bonds : bond 0.04096 / 2.72 ( 674) hydrogen bonds : angle 4.22355 / 3.03 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3076.35 seconds wall clock time: 53 minutes 21.85 seconds (3201.85 seconds total)