Starting phenix.real_space_refine on Wed Feb 4 10:01:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umg_64273/02_2026/9umg_64273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umg_64273/02_2026/9umg_64273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9umg_64273/02_2026/9umg_64273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umg_64273/02_2026/9umg_64273.map" model { file = "/net/cci-nas-00/data/ceres_data/9umg_64273/02_2026/9umg_64273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umg_64273/02_2026/9umg_64273.cif" } resolution = 3.04 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= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 38 5.16 5 C 6438 2.51 5 N 1639 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9877 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 865 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "B" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 819 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3354 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 21, 'TRANS': 390} Chain breaks: 1 Chain: "E" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3172 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain breaks: 7 Chain: "F" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'IHP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.19 Number of scatterers: 9877 At special positions: 0 Unit cell: (90.21, 118.11, 163.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 18 15.00 O 1744 8.00 N 1639 7.00 C 6438 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: 0.65 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 61.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.823A pdb=" N MET A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 89 removed outlier: 3.608A pdb=" N GLY A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'B' and resid 24 through 53 removed outlier: 3.591A pdb=" N ASN B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 40 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 90 removed outlier: 3.534A pdb=" N VAL B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 121 removed outlier: 4.078A pdb=" N ARG B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 54 removed outlier: 3.672A pdb=" N PHE C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 33 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 90 removed outlier: 3.538A pdb=" N VAL C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.527A pdb=" N ILE D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 303 through 309 Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.541A pdb=" N GLU D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 350 removed outlier: 3.614A pdb=" N ASN D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 447 removed outlier: 3.645A pdb=" N ARG D 442 " --> pdb=" O PRO D 438 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 444 " --> pdb=" O TRP D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 467 Processing helix chain 'D' and resid 477 through 481 removed outlier: 3.710A pdb=" N MET D 481 " --> pdb=" O LEU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 651 removed outlier: 3.868A pdb=" N TYR D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE D 625 " --> pdb=" O PRO D 621 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU D 628 " --> pdb=" O TYR D 624 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 659 removed outlier: 3.654A pdb=" N ILE D 658 " --> pdb=" O PRO D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 687 Processing helix chain 'D' and resid 696 through 719 removed outlier: 3.636A pdb=" N GLY D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.542A pdb=" N ARG E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 314 removed outlier: 3.743A pdb=" N ASN E 310 " --> pdb=" O PHE E 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E 312 " --> pdb=" O LEU E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.639A pdb=" N ASP E 332 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.652A pdb=" N ILE E 370 " --> pdb=" O ILE E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 386 removed outlier: 3.768A pdb=" N ARG E 386 " --> pdb=" O ILE E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 413 removed outlier: 4.188A pdb=" N LYS E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 Processing helix chain 'E' and resid 528 through 536 removed outlier: 3.626A pdb=" N ALA E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 553 removed outlier: 3.545A pdb=" N ASP E 552 " --> pdb=" O TRP E 549 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E 553 " --> pdb=" O LEU E 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 549 through 553' Processing helix chain 'E' and resid 697 through 726 removed outlier: 3.683A pdb=" N ILE E 724 " --> pdb=" O LEU E 720 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN E 726 " --> pdb=" O PHE E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 769 removed outlier: 3.743A pdb=" N ALA E 755 " --> pdb=" O CYS E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 806 removed outlier: 3.510A pdb=" N PHE E 799 " --> pdb=" O PHE E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 796 Processing helix chain 'F' and resid 806 through 835 removed outlier: 4.029A pdb=" N ASN F 810 " --> pdb=" O LEU F 806 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 811 " --> pdb=" O GLU F 807 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE F 835 " --> pdb=" O LEU F 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 842 through 869 removed outlier: 3.593A pdb=" N TYR F 846 " --> pdb=" O PRO F 842 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.896A pdb=" N ALA D 260 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR D 275 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR D 268 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 240 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 355 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP D 243 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D 360 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU D 379 " --> pdb=" O ASN D 360 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR D 362 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP D 377 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE D 364 " --> pdb=" O SER D 375 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER D 375 " --> pdb=" O PHE D 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 290 through 300 removed outlier: 7.052A pdb=" N THR D 275 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR D 268 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 240 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 355 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP D 243 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D 360 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU D 379 " --> pdb=" O ASN D 360 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR D 362 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP D 377 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE D 364 " --> pdb=" O SER D 375 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER D 375 " --> pdb=" O PHE D 364 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 199 " --> pdb=" O VAL D 427 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 221 through 223 removed outlier: 6.360A pdb=" N VAL D 221 " --> pdb=" O VAL E 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'E' and resid 206 through 211 removed outlier: 5.787A pdb=" N THR E 438 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE E 427 " --> pdb=" O THR E 438 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP E 440 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR E 425 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN E 442 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN E 423 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR E 300 " --> pdb=" O VAL E 417 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG E 419 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR E 298 " --> pdb=" O ARG E 419 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR E 421 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE E 296 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 297 " --> pdb=" O TRP E 326 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU E 322 " --> pdb=" O PHE E 301 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 336 " --> pdb=" O MET E 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 206 through 211 removed outlier: 4.695A pdb=" N ILE E 443 " --> pdb=" O PHE E 487 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1887 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: 1.46 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3025 1.34 - 1.46: 2415 1.46 - 1.58: 4585 1.58 - 1.70: 18 1.70 - 1.82: 63 Bond restraints: 10106 Sorted by residual: bond pdb=" CA LYS A 13 " pdb=" C LYS A 13 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.27e-02 6.20e+03 4.65e+00 bond pdb=" CA VAL D 424 " pdb=" C VAL D 424 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.14e-02 7.69e+03 3.46e+00 bond pdb=" CA ASN D 397 " pdb=" C ASN D 397 " ideal model delta sigma weight residual 1.520 1.499 0.021 1.20e-02 6.94e+03 3.17e+00 bond pdb=" CB ASN E 708 " pdb=" CG ASN E 708 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.94e+00 bond pdb=" CA ARG A 9 " pdb=" C ARG A 9 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.40e-02 5.10e+03 2.76e+00 ... (remaining 10101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 13400 2.40 - 4.80: 236 4.80 - 7.20: 44 7.20 - 9.60: 30 9.60 - 12.00: 5 Bond angle restraints: 13715 Sorted by residual: angle pdb=" CB MET B 70 " pdb=" CG MET B 70 " pdb=" SD MET B 70 " ideal model delta sigma weight residual 112.70 124.70 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CA GLU D 443 " pdb=" CB GLU D 443 " pdb=" CG GLU D 443 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CB MET D 329 " pdb=" CG MET D 329 " pdb=" SD MET D 329 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA TYR F 774 " pdb=" CB TYR F 774 " pdb=" CG TYR F 774 " ideal model delta sigma weight residual 113.90 120.58 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" C LEU E 550 " pdb=" N PRO E 551 " pdb=" CA PRO E 551 " ideal model delta sigma weight residual 121.65 118.08 3.57 1.01e+00 9.80e-01 1.25e+01 ... (remaining 13710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 5702 31.82 - 63.64: 290 63.64 - 95.47: 25 95.47 - 127.29: 18 127.29 - 159.11: 3 Dihedral angle restraints: 6038 sinusoidal: 2540 harmonic: 3498 Sorted by residual: dihedral pdb=" C4 IHP D 801 " pdb=" C2 IHP D 801 " pdb=" C3 IHP D 801 " pdb=" O12 IHP D 801 " ideal model delta sinusoidal sigma weight residual 60.90 -98.21 159.11 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C6 IHP D 802 " pdb=" C1 IHP D 802 " pdb=" C2 IHP D 802 " pdb=" O12 IHP D 802 " ideal model delta sinusoidal sigma weight residual 61.05 -150.19 -148.76 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C4 IHP D 802 " pdb=" C2 IHP D 802 " pdb=" C3 IHP D 802 " pdb=" O12 IHP D 802 " ideal model delta sinusoidal sigma weight residual 60.90 -171.23 -127.87 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 6035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 1553 0.997 - 1.994: 0 1.994 - 2.991: 0 2.991 - 3.988: 0 3.988 - 4.985: 12 Chirality restraints: 1565 Sorted by residual: chirality pdb=" C2 IHP D 801 " pdb=" C1 IHP D 801 " pdb=" C3 IHP D 801 " pdb=" O12 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.99 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C2 IHP D 802 " pdb=" C1 IHP D 802 " pdb=" C3 IHP D 802 " pdb=" O12 IHP D 802 " both_signs ideal model delta sigma weight residual False -2.52 2.44 -4.96 2.00e-01 2.50e+01 6.14e+02 chirality pdb=" C2 IHP E 901 " pdb=" C1 IHP E 901 " pdb=" C3 IHP E 901 " pdb=" O12 IHP E 901 " both_signs ideal model delta sigma weight residual False -2.52 2.41 -4.93 2.00e-01 2.50e+01 6.08e+02 ... (remaining 1562 not shown) Planarity restraints: 1670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 522 " 0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO E 523 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 523 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 523 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 698 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO D 699 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 699 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 699 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 779 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO E 780 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 780 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 780 " 0.029 5.00e-02 4.00e+02 ... (remaining 1667 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3961 2.93 - 3.42: 9778 3.42 - 3.92: 16357 3.92 - 4.41: 17657 4.41 - 4.90: 30011 Nonbonded interactions: 77764 Sorted by model distance: nonbonded pdb=" O11 IHP D 802 " pdb=" O16 IHP D 802 " model vdw 2.440 2.432 nonbonded pdb=" O15 IHP D 802 " pdb=" O16 IHP D 802 " model vdw 2.468 2.432 nonbonded pdb=" O15 IHP D 801 " pdb=" O16 IHP D 801 " model vdw 2.480 2.432 nonbonded pdb=" O11 IHP D 802 " pdb=" O12 IHP D 802 " model vdw 2.505 2.432 nonbonded pdb=" O12 IHP D 801 " pdb=" O13 IHP D 801 " model vdw 2.508 2.432 ... (remaining 77759 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 122) selection = (chain 'C' and (resid 21 through 89 or resid 99 through 122)) } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.860 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 0.043 10106 Z= 0.201 Angle : 0.853 11.996 13715 Z= 0.406 Chirality : 0.424 4.985 1565 Planarity : 0.006 0.071 1670 Dihedral : 19.573 159.108 3768 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.47 % Allowed : 30.01 % Favored : 69.52 % 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: -1.65 (0.22), residues: 1166 helix: -1.16 (0.16), residues: 681 sheet: -0.64 (0.43), residues: 161 loop : -0.63 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 480 TYR 0.034 0.002 TYR E 233 PHE 0.014 0.001 PHE D 409 TRP 0.009 0.001 TRP E 326 HIS 0.002 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00392 (10106) covalent geometry : angle 0.85320 (13715) hydrogen bonds : bond 0.20776 ( 614) hydrogen bonds : angle 8.44393 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 232 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.7743 (mt) cc_final: 0.7418 (mp) REVERT: D 336 GLU cc_start: 0.7136 (pt0) cc_final: 0.6453 (pt0) REVERT: D 378 THR cc_start: 0.8075 (t) cc_final: 0.7850 (p) REVERT: D 399 ARG cc_start: 0.7576 (ptt180) cc_final: 0.6619 (ptt180) REVERT: D 447 SER cc_start: 0.7998 (m) cc_final: 0.7757 (m) REVERT: D 680 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8435 (ttpt) REVERT: D 696 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7396 (mtmm) REVERT: E 367 ASN cc_start: 0.6382 (p0) cc_final: 0.6126 (p0) REVERT: E 368 ASN cc_start: 0.7284 (m110) cc_final: 0.6846 (m110) REVERT: E 487 PHE cc_start: 0.7801 (t80) cc_final: 0.7562 (t80) REVERT: E 521 GLU cc_start: 0.6438 (tm-30) cc_final: 0.6072 (tm-30) REVERT: E 735 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7829 (tm-30) REVERT: F 852 MET cc_start: 0.6970 (mpp) cc_final: 0.6562 (mpp) outliers start: 5 outliers final: 2 residues processed: 236 average time/residue: 0.1056 time to fit residues: 33.4619 Evaluate side-chains 202 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain E residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 244 ASN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128934 restraints weight = 14073.207| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.83 r_work: 0.3520 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10106 Z= 0.194 Angle : 0.840 18.267 13715 Z= 0.361 Chirality : 0.055 0.830 1565 Planarity : 0.005 0.047 1670 Dihedral : 11.910 125.587 1437 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.99 % Allowed : 22.95 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1166 helix: 0.97 (0.19), residues: 692 sheet: -0.53 (0.41), residues: 162 loop : -0.12 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 480 TYR 0.021 0.002 TYR F 774 PHE 0.030 0.002 PHE D 476 TRP 0.013 0.002 TRP E 326 HIS 0.006 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00428 (10106) covalent geometry : angle 0.84015 (13715) hydrogen bonds : bond 0.04111 ( 614) hydrogen bonds : angle 4.65288 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7356 (m) REVERT: B 70 MET cc_start: 0.8410 (mmp) cc_final: 0.7980 (mmp) REVERT: C 56 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7774 (ptpt) REVERT: C 73 MET cc_start: 0.8061 (ttp) cc_final: 0.7770 (ttp) REVERT: C 95 TYR cc_start: 0.7891 (m-80) cc_final: 0.7580 (m-80) REVERT: D 288 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7644 (t) REVERT: D 336 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6883 (pt0) REVERT: D 447 SER cc_start: 0.8403 (m) cc_final: 0.8181 (m) REVERT: D 456 PHE cc_start: 0.8132 (t80) cc_final: 0.7821 (t80) REVERT: D 658 ILE cc_start: 0.8694 (mm) cc_final: 0.8410 (mm) REVERT: D 696 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7603 (mtmm) REVERT: E 355 GLU cc_start: 0.6577 (tp30) cc_final: 0.6119 (tp30) REVERT: E 368 ASN cc_start: 0.7186 (m110) cc_final: 0.6832 (m110) REVERT: E 411 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6815 (mm-30) REVERT: E 418 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4651 (pp) REVERT: E 419 ARG cc_start: 0.7033 (mtp-110) cc_final: 0.6809 (mtp-110) REVERT: E 521 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5930 (tm-30) REVERT: E 772 LYS cc_start: 0.7754 (mmmm) cc_final: 0.7527 (mmmm) outliers start: 53 outliers final: 19 residues processed: 267 average time/residue: 0.1172 time to fit residues: 41.8518 Evaluate side-chains 240 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain F residue 770 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.153329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125702 restraints weight = 13811.331| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.84 r_work: 0.3469 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10106 Z= 0.163 Angle : 0.647 11.053 13715 Z= 0.299 Chirality : 0.047 0.467 1565 Planarity : 0.005 0.050 1670 Dihedral : 11.172 124.549 1437 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 5.36 % Allowed : 22.30 % Favored : 72.34 % 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: 1.44 (0.25), residues: 1166 helix: 1.73 (0.19), residues: 691 sheet: -0.20 (0.40), residues: 163 loop : -0.01 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 769 TYR 0.021 0.002 TYR F 774 PHE 0.029 0.002 PHE B 67 TRP 0.016 0.001 TRP E 326 HIS 0.005 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00381 (10106) covalent geometry : angle 0.64665 (13715) hydrogen bonds : bond 0.04209 ( 614) hydrogen bonds : angle 4.29555 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7470 (m) REVERT: A 43 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 39 PHE cc_start: 0.8522 (m-80) cc_final: 0.8262 (m-80) REVERT: B 70 MET cc_start: 0.8496 (mmp) cc_final: 0.8125 (mmp) REVERT: C 73 MET cc_start: 0.8175 (ttp) cc_final: 0.7944 (ttp) REVERT: C 95 TYR cc_start: 0.8019 (m-80) cc_final: 0.7760 (m-80) REVERT: D 268 TYR cc_start: 0.8462 (m-80) cc_final: 0.8226 (m-80) REVERT: D 336 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6840 (pt0) REVERT: D 373 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: D 387 ASN cc_start: 0.6131 (p0) cc_final: 0.5446 (m-40) REVERT: D 447 SER cc_start: 0.8463 (m) cc_final: 0.8247 (m) REVERT: D 456 PHE cc_start: 0.8410 (t80) cc_final: 0.7566 (t80) REVERT: D 658 ILE cc_start: 0.8801 (mm) cc_final: 0.8512 (mm) REVERT: D 689 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7327 (mtp85) REVERT: D 696 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7588 (mtmm) REVERT: D 701 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: D 722 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6242 (pp) REVERT: E 206 LYS cc_start: 0.6550 (tttp) cc_final: 0.6296 (tttp) REVERT: E 325 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8114 (mtp-110) REVERT: E 387 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: E 419 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7044 (mtp180) REVERT: E 521 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6111 (tm-30) REVERT: E 535 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4639 (tm) REVERT: E 725 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7141 (t80) REVERT: E 748 THR cc_start: 0.8143 (m) cc_final: 0.7425 (p) REVERT: E 791 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7910 (tt) outliers start: 57 outliers final: 32 residues processed: 261 average time/residue: 0.1175 time to fit residues: 41.5178 Evaluate side-chains 251 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 402 PHE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 725 TYR Chi-restraints excluded: chain E residue 735 GLN Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 775 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 0.0040 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 HIS ** E 726 ASN ** 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 = 0.3960 r_free = 0.3960 target = 0.151571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124517 restraints weight = 13787.332| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.78 r_work: 0.3460 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10106 Z= 0.156 Angle : 0.594 14.120 13715 Z= 0.283 Chirality : 0.044 0.385 1565 Planarity : 0.005 0.050 1670 Dihedral : 9.394 87.706 1437 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 5.27 % Allowed : 22.01 % Favored : 72.72 % 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: 1.64 (0.25), residues: 1166 helix: 1.92 (0.19), residues: 694 sheet: -0.17 (0.40), residues: 162 loop : -0.00 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 769 TYR 0.021 0.002 TYR F 774 PHE 0.021 0.002 PHE B 67 TRP 0.017 0.001 TRP E 326 HIS 0.005 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00366 (10106) covalent geometry : angle 0.59433 (13715) hydrogen bonds : bond 0.03802 ( 614) hydrogen bonds : angle 4.10939 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7645 (OUTLIER) cc_final: 0.7411 (m) REVERT: A 70 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7552 (mpp) REVERT: B 39 PHE cc_start: 0.8528 (m-80) cc_final: 0.8201 (m-80) REVERT: B 70 MET cc_start: 0.8558 (mmp) cc_final: 0.8046 (mmp) REVERT: C 42 MET cc_start: 0.7787 (tmm) cc_final: 0.7572 (ttm) REVERT: C 73 MET cc_start: 0.8258 (ttp) cc_final: 0.7993 (ttp) REVERT: C 95 TYR cc_start: 0.8004 (m-80) cc_final: 0.7753 (m-80) REVERT: D 274 ASP cc_start: 0.7696 (p0) cc_final: 0.7446 (p0) REVERT: D 288 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8014 (p) REVERT: D 336 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6841 (pt0) REVERT: D 373 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: D 447 SER cc_start: 0.8464 (m) cc_final: 0.8242 (m) REVERT: D 456 PHE cc_start: 0.8489 (t80) cc_final: 0.7701 (t80) REVERT: D 689 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7389 (mtp85) REVERT: D 696 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7568 (mtmm) REVERT: D 706 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7596 (mp) REVERT: D 722 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6352 (pp) REVERT: E 206 LYS cc_start: 0.6886 (tttp) cc_final: 0.6499 (tttp) REVERT: E 209 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7389 (mtpp) REVERT: E 432 ASP cc_start: 0.7267 (t0) cc_final: 0.7044 (t0) REVERT: E 444 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6414 (mtt) REVERT: E 521 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6069 (tm-30) REVERT: E 525 PHE cc_start: 0.7848 (t80) cc_final: 0.7528 (t80) REVERT: E 535 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.4648 (tm) REVERT: E 791 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8039 (tt) outliers start: 56 outliers final: 36 residues processed: 256 average time/residue: 0.0903 time to fit residues: 31.9418 Evaluate side-chains 269 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 402 PHE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 735 GLN Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 857 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.0030 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 244 ASN E 368 ASN ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124662 restraints weight = 13738.598| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.84 r_work: 0.3471 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10106 Z= 0.132 Angle : 0.552 12.582 13715 Z= 0.265 Chirality : 0.043 0.347 1565 Planarity : 0.004 0.050 1670 Dihedral : 9.443 85.766 1437 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 5.64 % Allowed : 21.92 % Favored : 72.44 % 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: 1.94 (0.25), residues: 1166 helix: 2.14 (0.19), residues: 694 sheet: 0.14 (0.41), residues: 159 loop : 0.04 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 769 TYR 0.021 0.002 TYR F 774 PHE 0.028 0.001 PHE E 427 TRP 0.015 0.001 TRP E 326 HIS 0.003 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00304 (10106) covalent geometry : angle 0.55190 (13715) hydrogen bonds : bond 0.03654 ( 614) hydrogen bonds : angle 3.93142 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7482 (m) REVERT: A 70 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7593 (mpp) REVERT: B 39 PHE cc_start: 0.8510 (m-80) cc_final: 0.8182 (m-80) REVERT: B 70 MET cc_start: 0.8564 (mmp) cc_final: 0.8173 (mmp) REVERT: C 73 MET cc_start: 0.8278 (ttp) cc_final: 0.8039 (ttp) REVERT: C 95 TYR cc_start: 0.8021 (m-80) cc_final: 0.7771 (m-80) REVERT: D 274 ASP cc_start: 0.7764 (p0) cc_final: 0.7525 (p0) REVERT: D 336 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: D 447 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8251 (m) REVERT: D 476 PHE cc_start: 0.8515 (p90) cc_final: 0.8283 (p90) REVERT: D 689 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7442 (mtp85) REVERT: D 696 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7584 (mtmm) REVERT: D 722 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6536 (pp) REVERT: E 206 LYS cc_start: 0.6955 (tttp) cc_final: 0.6534 (tttp) REVERT: E 209 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7462 (mtpp) REVERT: E 221 LYS cc_start: 0.7334 (ttmt) cc_final: 0.7113 (mttt) REVERT: E 383 ASN cc_start: 0.7606 (m-40) cc_final: 0.7101 (m-40) REVERT: E 387 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: E 419 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.7220 (mtp180) REVERT: E 423 ASN cc_start: 0.7169 (m-40) cc_final: 0.6887 (m-40) REVERT: E 444 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6394 (mtt) REVERT: E 521 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5969 (tm-30) REVERT: E 525 PHE cc_start: 0.8010 (t80) cc_final: 0.7610 (t80) REVERT: E 535 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4738 (tm) REVERT: E 791 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7980 (tt) REVERT: E 806 GLU cc_start: 0.6061 (pp20) cc_final: 0.5737 (pp20) outliers start: 60 outliers final: 36 residues processed: 267 average time/residue: 0.1044 time to fit residues: 37.4455 Evaluate side-chains 264 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 305 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 402 PHE Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 700 TRP Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 857 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 218 HIS D 225 ASN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.150399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123719 restraints weight = 13757.133| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.75 r_work: 0.3465 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10106 Z= 0.155 Angle : 0.577 11.572 13715 Z= 0.279 Chirality : 0.043 0.231 1565 Planarity : 0.005 0.052 1670 Dihedral : 9.594 83.496 1437 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.64 % Allowed : 21.45 % Favored : 72.91 % 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: 1.91 (0.25), residues: 1166 helix: 2.10 (0.19), residues: 695 sheet: 0.04 (0.40), residues: 161 loop : 0.15 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 769 TYR 0.020 0.002 TYR F 774 PHE 0.018 0.002 PHE B 67 TRP 0.019 0.001 TRP E 326 HIS 0.003 0.001 HIS F 845 Details of bonding type rmsd covalent geometry : bond 0.00364 (10106) covalent geometry : angle 0.57731 (13715) hydrogen bonds : bond 0.03816 ( 614) hydrogen bonds : angle 3.95809 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7494 (m) REVERT: A 70 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7599 (mpp) REVERT: B 39 PHE cc_start: 0.8491 (m-80) cc_final: 0.8177 (m-80) REVERT: B 70 MET cc_start: 0.8558 (mmp) cc_final: 0.8346 (mmp) REVERT: C 73 MET cc_start: 0.8292 (ttp) cc_final: 0.8050 (ttp) REVERT: C 95 TYR cc_start: 0.8020 (m-80) cc_final: 0.7774 (m-80) REVERT: C 96 ASP cc_start: 0.7622 (t70) cc_final: 0.7335 (t70) REVERT: D 223 VAL cc_start: 0.7899 (t) cc_final: 0.7639 (p) REVERT: D 227 ASN cc_start: 0.8208 (t0) cc_final: 0.7986 (t0) REVERT: D 274 ASP cc_start: 0.7760 (p0) cc_final: 0.7495 (p0) REVERT: D 336 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: D 351 LEU cc_start: 0.7883 (mt) cc_final: 0.7482 (mp) REVERT: D 447 SER cc_start: 0.8458 (m) cc_final: 0.8254 (m) REVERT: D 476 PHE cc_start: 0.8505 (p90) cc_final: 0.8265 (p90) REVERT: D 696 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7446 (mtmm) REVERT: D 722 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6571 (pp) REVERT: E 206 LYS cc_start: 0.7097 (tttp) cc_final: 0.6650 (tttp) REVERT: E 325 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.7966 (mtp-110) REVERT: E 383 ASN cc_start: 0.7684 (m-40) cc_final: 0.7009 (m-40) REVERT: E 387 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: E 419 ARG cc_start: 0.7554 (mtp-110) cc_final: 0.7253 (mtp180) REVERT: E 423 ASN cc_start: 0.7199 (m-40) cc_final: 0.6852 (m-40) REVERT: E 444 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6353 (mtt) REVERT: E 521 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5913 (tm-30) REVERT: E 525 PHE cc_start: 0.8102 (t80) cc_final: 0.7793 (t80) REVERT: E 535 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4640 (tm) REVERT: E 791 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8109 (tt) REVERT: E 806 GLU cc_start: 0.6178 (pp20) cc_final: 0.5888 (pp20) outliers start: 60 outliers final: 38 residues processed: 268 average time/residue: 0.1112 time to fit residues: 39.4391 Evaluate side-chains 272 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 402 PHE Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 700 TRP Chi-restraints excluded: chain E residue 751 CYS Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 857 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 0.0870 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.0970 chunk 73 optimal weight: 0.1980 chunk 93 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN D 244 ASN D 303 HIS ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125313 restraints weight = 13863.571| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.78 r_work: 0.3490 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10106 Z= 0.109 Angle : 0.554 15.758 13715 Z= 0.263 Chirality : 0.041 0.254 1565 Planarity : 0.004 0.056 1670 Dihedral : 9.502 82.362 1437 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 5.08 % Allowed : 22.20 % Favored : 72.72 % 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: 2.27 (0.25), residues: 1166 helix: 2.40 (0.19), residues: 695 sheet: 0.18 (0.40), residues: 166 loop : 0.25 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 419 TYR 0.022 0.001 TYR F 774 PHE 0.020 0.001 PHE B 67 TRP 0.015 0.001 TRP E 326 HIS 0.004 0.001 HIS E 773 Details of bonding type rmsd covalent geometry : bond 0.00246 (10106) covalent geometry : angle 0.55374 (13715) hydrogen bonds : bond 0.03437 ( 614) hydrogen bonds : angle 3.77303 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (m) REVERT: A 70 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7524 (mpp) REVERT: B 70 MET cc_start: 0.8556 (mmp) cc_final: 0.8280 (mmp) REVERT: C 95 TYR cc_start: 0.8015 (m-80) cc_final: 0.7775 (m-80) REVERT: C 96 ASP cc_start: 0.7606 (t70) cc_final: 0.7267 (t70) REVERT: D 227 ASN cc_start: 0.8217 (t0) cc_final: 0.7980 (t0) REVERT: D 274 ASP cc_start: 0.7767 (p0) cc_final: 0.7517 (p0) REVERT: D 288 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7962 (p) REVERT: D 336 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6876 (pt0) REVERT: D 351 LEU cc_start: 0.7971 (mt) cc_final: 0.7467 (mp) REVERT: D 447 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8231 (m) REVERT: D 476 PHE cc_start: 0.8468 (p90) cc_final: 0.8214 (p90) REVERT: D 689 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7546 (mtt-85) REVERT: D 696 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7499 (mtmm) REVERT: D 701 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7865 (ptm) REVERT: E 206 LYS cc_start: 0.7034 (tttp) cc_final: 0.6579 (tttp) REVERT: E 209 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7438 (mmmm) REVERT: E 325 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7948 (mtp-110) REVERT: E 383 ASN cc_start: 0.7716 (m-40) cc_final: 0.7149 (m-40) REVERT: E 387 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: E 419 ARG cc_start: 0.7553 (mtp-110) cc_final: 0.7244 (mtp180) REVERT: E 423 ASN cc_start: 0.7188 (m-40) cc_final: 0.6814 (t0) REVERT: E 432 ASP cc_start: 0.7281 (t0) cc_final: 0.6814 (t0) REVERT: E 444 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6383 (mtt) REVERT: E 494 ILE cc_start: 0.7380 (mt) cc_final: 0.6945 (tt) REVERT: E 508 GLU cc_start: 0.5807 (mm-30) cc_final: 0.5317 (tp30) REVERT: E 521 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: E 525 PHE cc_start: 0.8148 (t80) cc_final: 0.7873 (t80) REVERT: E 535 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4528 (tm) REVERT: E 791 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7995 (tt) REVERT: E 806 GLU cc_start: 0.6097 (pp20) cc_final: 0.5828 (pp20) outliers start: 54 outliers final: 30 residues processed: 259 average time/residue: 0.1096 time to fit residues: 37.6033 Evaluate side-chains 263 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 700 TRP Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 808 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 14 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 244 ASN D 303 HIS ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123902 restraints weight = 13758.137| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.76 r_work: 0.3470 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10106 Z= 0.142 Angle : 0.568 15.514 13715 Z= 0.272 Chirality : 0.042 0.242 1565 Planarity : 0.005 0.059 1670 Dihedral : 9.400 81.033 1437 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 5.64 % Allowed : 21.35 % Favored : 73.00 % 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: 2.20 (0.25), residues: 1166 helix: 2.33 (0.19), residues: 695 sheet: 0.24 (0.41), residues: 162 loop : 0.18 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 119 TYR 0.021 0.002 TYR F 774 PHE 0.024 0.001 PHE E 427 TRP 0.016 0.001 TRP E 326 HIS 0.014 0.002 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00334 (10106) covalent geometry : angle 0.56820 (13715) hydrogen bonds : bond 0.03629 ( 614) hydrogen bonds : angle 3.83735 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7509 (m) REVERT: A 70 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7507 (mpp) REVERT: B 70 MET cc_start: 0.8555 (mmp) cc_final: 0.8267 (mmp) REVERT: C 95 TYR cc_start: 0.8029 (m-80) cc_final: 0.7782 (m-80) REVERT: C 96 ASP cc_start: 0.7615 (t70) cc_final: 0.7287 (t70) REVERT: D 223 VAL cc_start: 0.7886 (t) cc_final: 0.7645 (p) REVERT: D 227 ASN cc_start: 0.8249 (t0) cc_final: 0.7928 (t0) REVERT: D 274 ASP cc_start: 0.7784 (p0) cc_final: 0.7538 (p0) REVERT: D 336 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6872 (pt0) REVERT: D 351 LEU cc_start: 0.8049 (mt) cc_final: 0.7562 (mp) REVERT: D 447 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8297 (m) REVERT: D 476 PHE cc_start: 0.8492 (p90) cc_final: 0.8239 (p90) REVERT: D 689 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7543 (mtt-85) REVERT: D 696 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7443 (mtmm) REVERT: D 722 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6504 (pp) REVERT: E 206 LYS cc_start: 0.7071 (tttp) cc_final: 0.6620 (tttp) REVERT: E 209 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7499 (mtpp) REVERT: E 221 LYS cc_start: 0.7424 (ttmt) cc_final: 0.7178 (mttt) REVERT: E 325 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.7899 (mtp-110) REVERT: E 379 ASN cc_start: 0.5739 (OUTLIER) cc_final: 0.5363 (p0) REVERT: E 383 ASN cc_start: 0.7774 (m-40) cc_final: 0.7046 (m-40) REVERT: E 387 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: E 419 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7301 (mtp180) REVERT: E 423 ASN cc_start: 0.7210 (m-40) cc_final: 0.6877 (m-40) REVERT: E 444 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6373 (mtt) REVERT: E 494 ILE cc_start: 0.7477 (mt) cc_final: 0.7053 (tt) REVERT: E 495 LYS cc_start: 0.7515 (mttt) cc_final: 0.7208 (mttt) REVERT: E 508 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5403 (tp30) REVERT: E 521 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5897 (tm-30) REVERT: E 525 PHE cc_start: 0.8245 (t80) cc_final: 0.7892 (t80) REVERT: E 535 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4724 (tm) REVERT: E 791 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (tt) REVERT: E 806 GLU cc_start: 0.6098 (pp20) cc_final: 0.5845 (pp20) outliers start: 60 outliers final: 43 residues processed: 255 average time/residue: 0.1107 time to fit residues: 37.6737 Evaluate side-chains 276 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 700 TRP Chi-restraints excluded: chain E residue 751 CYS Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 808 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 117 optimal weight: 0.9980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 244 ASN D 303 HIS ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124525 restraints weight = 13804.928| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.74 r_work: 0.3478 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10106 Z= 0.136 Angle : 0.571 15.091 13715 Z= 0.272 Chirality : 0.042 0.243 1565 Planarity : 0.005 0.061 1670 Dihedral : 9.260 79.837 1437 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.55 % Allowed : 21.83 % Favored : 72.62 % 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: 2.18 (0.25), residues: 1166 helix: 2.32 (0.19), residues: 697 sheet: 0.30 (0.41), residues: 161 loop : 0.14 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 769 TYR 0.021 0.002 TYR F 774 PHE 0.026 0.001 PHE E 427 TRP 0.015 0.001 TRP E 326 HIS 0.008 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00317 (10106) covalent geometry : angle 0.57062 (13715) hydrogen bonds : bond 0.03604 ( 614) hydrogen bonds : angle 3.82002 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7506 (m) REVERT: A 70 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7527 (mpp) REVERT: B 70 MET cc_start: 0.8576 (mmp) cc_final: 0.8330 (mmp) REVERT: C 95 TYR cc_start: 0.8024 (m-80) cc_final: 0.7784 (m-80) REVERT: C 96 ASP cc_start: 0.7607 (t70) cc_final: 0.7290 (t70) REVERT: D 223 VAL cc_start: 0.7903 (t) cc_final: 0.7672 (p) REVERT: D 227 ASN cc_start: 0.8242 (t0) cc_final: 0.8009 (t0) REVERT: D 274 ASP cc_start: 0.7740 (p0) cc_final: 0.7487 (p0) REVERT: D 336 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: D 351 LEU cc_start: 0.8096 (mt) cc_final: 0.7619 (mp) REVERT: D 447 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8302 (m) REVERT: D 476 PHE cc_start: 0.8488 (p90) cc_final: 0.8247 (p90) REVERT: D 689 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7514 (mtt-85) REVERT: D 696 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7410 (mtmm) REVERT: D 722 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6632 (pp) REVERT: E 206 LYS cc_start: 0.7179 (tttp) cc_final: 0.6714 (tttp) REVERT: E 209 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7484 (mtpp) REVERT: E 221 LYS cc_start: 0.7447 (ttmt) cc_final: 0.7235 (mttt) REVERT: E 325 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7938 (mtp-110) REVERT: E 379 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.5531 (p0) REVERT: E 383 ASN cc_start: 0.7670 (m-40) cc_final: 0.7138 (m-40) REVERT: E 387 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: E 419 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7331 (mtp180) REVERT: E 423 ASN cc_start: 0.7192 (m-40) cc_final: 0.6844 (m-40) REVERT: E 432 ASP cc_start: 0.7286 (t0) cc_final: 0.6814 (t0) REVERT: E 444 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6358 (mtt) REVERT: E 494 ILE cc_start: 0.7562 (mt) cc_final: 0.7129 (tt) REVERT: E 495 LYS cc_start: 0.7512 (mttt) cc_final: 0.7224 (mttt) REVERT: E 508 GLU cc_start: 0.5874 (mm-30) cc_final: 0.5400 (tp30) REVERT: E 521 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5845 (tm-30) REVERT: E 525 PHE cc_start: 0.8380 (t80) cc_final: 0.7999 (t80) REVERT: E 535 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4727 (tm) REVERT: E 791 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8103 (tt) REVERT: E 806 GLU cc_start: 0.6154 (pp20) cc_final: 0.5914 (pp20) outliers start: 59 outliers final: 41 residues processed: 262 average time/residue: 0.1077 time to fit residues: 37.5471 Evaluate side-chains 282 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 497 ILE Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 700 TRP Chi-restraints excluded: chain E residue 735 GLN Chi-restraints excluded: chain E residue 751 CYS Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 808 ILE Chi-restraints excluded: chain F residue 857 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 244 ASN D 303 HIS ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124047 restraints weight = 13665.212| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.78 r_work: 0.3467 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10106 Z= 0.147 Angle : 0.579 14.832 13715 Z= 0.276 Chirality : 0.042 0.237 1565 Planarity : 0.005 0.062 1670 Dihedral : 9.119 78.234 1437 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.27 % Allowed : 22.20 % Favored : 72.53 % 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: 2.13 (0.25), residues: 1166 helix: 2.29 (0.19), residues: 697 sheet: 0.25 (0.41), residues: 161 loop : 0.10 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 769 TYR 0.021 0.002 TYR F 774 PHE 0.026 0.002 PHE E 427 TRP 0.016 0.001 TRP E 326 HIS 0.012 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00346 (10106) covalent geometry : angle 0.57932 (13715) hydrogen bonds : bond 0.03672 ( 614) hydrogen bonds : angle 3.82735 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7521 (m) REVERT: A 70 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7514 (mpp) REVERT: B 39 PHE cc_start: 0.8515 (m-80) cc_final: 0.8149 (m-80) REVERT: B 70 MET cc_start: 0.8556 (mmp) cc_final: 0.8309 (mmp) REVERT: C 95 TYR cc_start: 0.8062 (m-80) cc_final: 0.7820 (m-80) REVERT: C 96 ASP cc_start: 0.7600 (t70) cc_final: 0.7221 (t70) REVERT: D 223 VAL cc_start: 0.7904 (t) cc_final: 0.7669 (p) REVERT: D 227 ASN cc_start: 0.8275 (t0) cc_final: 0.8039 (t0) REVERT: D 274 ASP cc_start: 0.7782 (p0) cc_final: 0.7517 (p0) REVERT: D 336 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6896 (pt0) REVERT: D 351 LEU cc_start: 0.8133 (mt) cc_final: 0.7667 (mp) REVERT: D 447 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 451 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6935 (tm-30) REVERT: D 476 PHE cc_start: 0.8492 (p90) cc_final: 0.8253 (p90) REVERT: D 689 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7524 (mtt-85) REVERT: D 696 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7455 (mtmm) REVERT: D 722 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6701 (pp) REVERT: E 206 LYS cc_start: 0.7211 (tttp) cc_final: 0.6727 (tttp) REVERT: E 209 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7499 (mtpp) REVERT: E 221 LYS cc_start: 0.7459 (ttmt) cc_final: 0.7195 (mttt) REVERT: E 325 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.7941 (mtp-110) REVERT: E 379 ASN cc_start: 0.5777 (OUTLIER) cc_final: 0.5572 (p0) REVERT: E 383 ASN cc_start: 0.7820 (m-40) cc_final: 0.7272 (m-40) REVERT: E 387 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: E 419 ARG cc_start: 0.7579 (mtp-110) cc_final: 0.7113 (mtp180) REVERT: E 423 ASN cc_start: 0.7199 (m-40) cc_final: 0.6866 (m-40) REVERT: E 432 ASP cc_start: 0.7345 (t0) cc_final: 0.6855 (t0) REVERT: E 444 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6386 (mtt) REVERT: E 495 LYS cc_start: 0.7510 (mttt) cc_final: 0.7203 (mttt) REVERT: E 508 GLU cc_start: 0.5864 (mm-30) cc_final: 0.5409 (tp30) REVERT: E 521 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5853 (tm-30) REVERT: E 535 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4732 (tm) REVERT: E 791 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8091 (tt) REVERT: E 806 GLU cc_start: 0.6151 (pp20) cc_final: 0.5905 (pp20) outliers start: 56 outliers final: 42 residues processed: 261 average time/residue: 0.1071 time to fit residues: 36.8477 Evaluate side-chains 283 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 486 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 497 ILE Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 700 TRP Chi-restraints excluded: chain E residue 735 GLN Chi-restraints excluded: chain E residue 751 CYS Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 791 LEU Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 808 ILE Chi-restraints excluded: chain F residue 857 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 96 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 244 ASN D 303 HIS ** E 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122642 restraints weight = 13669.511| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.82 r_work: 0.3453 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10106 Z= 0.157 Angle : 0.588 14.680 13715 Z= 0.280 Chirality : 0.042 0.232 1565 Planarity : 0.005 0.062 1670 Dihedral : 9.007 76.597 1437 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.08 % Allowed : 22.86 % Favored : 72.06 % 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: 2.06 (0.25), residues: 1166 helix: 2.23 (0.19), residues: 697 sheet: 0.22 (0.41), residues: 161 loop : 0.06 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 769 TYR 0.021 0.002 TYR F 774 PHE 0.027 0.002 PHE E 427 TRP 0.016 0.001 TRP E 326 HIS 0.006 0.001 HIS E 773 Details of bonding type rmsd covalent geometry : bond 0.00369 (10106) covalent geometry : angle 0.58792 (13715) hydrogen bonds : bond 0.03744 ( 614) hydrogen bonds : angle 3.85642 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.44 seconds wall clock time: 50 minutes 32.43 seconds (3032.43 seconds total)