Starting phenix.real_space_refine on Thu Aug 6 08:48:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8siy_40522/08_2026/8siy_40522.map" } resolution = 2.9 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= 0.045 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 294 5.49 5 S 33 5.16 5 C 8443 2.51 5 N 2738 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14844 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2654 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 18, 'TRANS': 322} Chain breaks: 4 Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "D" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "H" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2993 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 2.89, per 1000 atoms: 0.19 Number of scatterers: 14844 At special positions: 0 Unit cell: (112.32, 114.816, 123.136, 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 33 16.00 P 294 15.00 O 3336 8.00 N 2738 7.00 C 8443 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: 1.09 Conformation dependent library (CDL) restraints added in 328.8 milliseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 18 sheets defined 51.3% alpha, 14.2% beta 144 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.678A pdb=" N ASN A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'C' and resid 44 through 57 Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.785A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.524A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.612A pdb=" N GLN D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.613A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 16 through 22 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 45 through 73 removed outlier: 4.378A pdb=" N VAL E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.516A pdb=" N LEU E 83 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'F' and resid 37 through 49 Processing helix chain 'F' and resid 55 through 84 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 103 through 124 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 77 removed outlier: 3.927A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 46 through 72 removed outlier: 3.544A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 37 through 49 Processing helix chain 'J' and resid 55 through 84 Processing helix chain 'J' and resid 90 through 102 Processing helix chain 'J' and resid 103 through 124 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.595A pdb=" N VAL B 22 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 621 through 626 removed outlier: 3.769A pdb=" N THR A 623 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 642 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 276 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 644 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLN B 15 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 276 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298 removed outlier: 3.794A pdb=" N ALA A 295 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 321 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP A 326 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 332 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 335 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.602A pdb=" N SER A 345 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 387 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 379 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N CYS A 385 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 400 removed outlier: 3.882A pdb=" N ARG A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 418 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 439 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 420 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 451 removed outlier: 6.362A pdb=" N GLY A 463 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 449 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 461 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 459 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS A 468 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASN A 487 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 506 removed outlier: 6.110A pdb=" N ILE A 522 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN A 547 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 524 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563 removed outlier: 3.507A pdb=" N LEU A 568 " --> pdb=" O CYS A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.871A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.640A pdb=" N THR D 96 " --> pdb=" O THR I 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 42 through 43 removed outlier: 7.261A pdb=" N ARG E 42 " --> pdb=" O ILE F 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.216A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.442A pdb=" N ARG I 42 " --> pdb=" O ILE J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 77 through 78 501 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 742 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3004 1.33 - 1.45: 4707 1.45 - 1.57: 7384 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 15728 Sorted by residual: bond pdb=" C3' DG L 4 " pdb=" C2' DG L 4 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" C3' DT L 67 " pdb=" C2' DT L 67 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C1' DT K -72 " pdb=" N1 DT K -72 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C3' DA K -66 " pdb=" C2' DA K -66 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DG L -19 " pdb=" C2' DG L -19 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 ... (remaining 15723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 21459 1.78 - 3.56: 1029 3.56 - 5.33: 55 5.33 - 7.11: 2 7.11 - 8.89: 2 Bond angle restraints: 22547 Sorted by residual: angle pdb=" O4' DG K 47 " pdb=" C4' DG K 47 " pdb=" C3' DG K 47 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.41e+01 angle pdb=" N3 DT K 43 " pdb=" C4 DT K 43 " pdb=" O4 DT K 43 " ideal model delta sigma weight residual 119.90 122.80 -2.90 6.00e-01 2.78e+00 2.34e+01 angle pdb=" O4' DC K -2 " pdb=" C1' DC K -2 " pdb=" N1 DC K -2 " ideal model delta sigma weight residual 108.00 111.37 -3.37 7.00e-01 2.04e+00 2.32e+01 angle pdb=" N3 DT K -72 " pdb=" C4 DT K -72 " pdb=" O4 DT K -72 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT L -50 " pdb=" C4 DT L -50 " pdb=" O4 DT L -50 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 22542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 7142 34.08 - 68.16: 1490 68.16 - 102.23: 14 102.23 - 136.31: 2 136.31 - 170.39: 2 Dihedral angle restraints: 8650 sinusoidal: 5411 harmonic: 3239 Sorted by residual: dihedral pdb=" C4' DC L -58 " pdb=" C3' DC L -58 " pdb=" O3' DC L -58 " pdb=" P DT L -57 " ideal model delta sinusoidal sigma weight residual 220.00 49.61 170.39 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG L 20 " pdb=" C3' DG L 20 " pdb=" O3' DG L 20 " pdb=" P DG L 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.40 153.60 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA GLU A 406 " pdb=" C GLU A 406 " pdb=" N THR A 407 " pdb=" CA THR A 407 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1702 0.042 - 0.083: 468 0.083 - 0.125: 154 0.125 - 0.166: 202 0.166 - 0.208: 49 Chirality restraints: 2575 Sorted by residual: chirality pdb=" C3' DC L 49 " pdb=" C4' DC L 49 " pdb=" O3' DC L 49 " pdb=" C2' DC L 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3' DC K 49 " pdb=" C4' DC K 49 " pdb=" O3' DC K 49 " pdb=" C2' DC K 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DC K 8 " pdb=" C4' DC K 8 " pdb=" O3' DC K 8 " pdb=" C2' DC K 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2572 not shown) Planarity restraints: 1830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 598 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 599 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 599 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 599 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 450 " 0.045 5.00e-02 4.00e+02 6.93e-02 7.67e+00 pdb=" N PRO A 451 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 272 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO A 273 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.033 5.00e-02 4.00e+02 ... (remaining 1827 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 61 2.57 - 3.16: 11356 3.16 - 3.74: 26526 3.74 - 4.32: 37287 4.32 - 4.90: 54158 Nonbonded interactions: 129388 Sorted by model distance: nonbonded pdb=" OG1 THR F 90 " pdb=" OE1 GLU F 93 " model vdw 1.993 3.040 nonbonded pdb=" OE2 GLU A 299 " pdb=" ND2 ASN A 364 " model vdw 2.068 3.120 nonbonded pdb=" OG1 THR J 90 " pdb=" OE1 GLU J 93 " model vdw 2.087 3.040 nonbonded pdb=" NE2 GLN A 292 " pdb=" O ARG H 19 " model vdw 2.093 3.120 nonbonded pdb=" OG SER A 561 " pdb=" O VAL A 624 " model vdw 2.167 3.040 ... (remaining 129383 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 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 24 through 102) } ncs_group { reference = (chain 'E' and resid 11 through 117) selection = chain 'I' } ncs_group { reference = (chain 'F' and resid 32 through 124) selection = chain 'J' } 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.980 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.007 0.078 15728 Z= 0.587 Angle : 0.783 8.890 22547 Z= 0.645 Chirality : 0.062 0.208 2575 Planarity : 0.006 0.102 1830 Dihedral : 26.203 170.390 6552 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.38 % Allowed : 9.14 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1087 helix: 2.11 (0.21), residues: 554 sheet: 0.38 (0.48), residues: 113 loop : -0.58 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 92 TYR 0.012 0.002 TYR J 121 PHE 0.008 0.001 PHE C 84 TRP 0.008 0.001 TRP A 645 HIS 0.011 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.59 (15728) covalent geometry : angle 0.78273 / 0.65 (22547) hydrogen bonds : bond 0.11521 / 8.22 ( 872) hydrogen bonds : angle 4.40506 / 3.03 ( 2185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 0.427 Fit side-chains REVERT: F 42 TYR cc_start: 0.8075 (t80) cc_final: 0.7824 (t80) REVERT: I 73 ASN cc_start: 0.8454 (t0) cc_final: 0.8203 (t0) REVERT: J 42 TYR cc_start: 0.8031 (t80) cc_final: 0.7617 (t80) outliers start: 13 outliers final: 3 residues processed: 278 average time/residue: 0.7336 time to fit residues: 219.7851 Evaluate side-chains 175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 529 GLN A 567 ASN C 76 GLN C 108 ASN E 73 ASN F 47 GLN G 76 GLN G 108 ASN I 112 GLN J 49 HIS J 67 ASN B 15 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051230 restraints weight = 43304.556| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.28 r_work: 0.2651 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15728 Z= 0.222 Angle : 0.732 9.213 22547 Z= 0.407 Chirality : 0.047 0.241 2575 Planarity : 0.005 0.054 1830 Dihedral : 30.056 171.908 4438 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.72 % Allowed : 17.00 % Favored : 79.28 % 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 (0.25), residues: 1087 helix: 2.47 (0.21), residues: 557 sheet: 0.35 (0.48), residues: 118 loop : -0.64 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 381 TYR 0.020 0.002 TYR A 336 PHE 0.014 0.002 PHE A 630 TRP 0.015 0.002 TRP A 471 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (15728) covalent geometry : angle 0.73202 / 0.41 (22547) hydrogen bonds : bond 0.04911 / 3.36 ( 872) hydrogen bonds : angle 3.70174 / 2.54 ( 2185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.419 Fit side-chains REVERT: A 275 HIS cc_start: 0.7195 (m-70) cc_final: 0.6868 (m-70) REVERT: A 567 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8068 (t0) REVERT: A 620 MET cc_start: 0.8014 (mtm) cc_final: 0.7729 (ttp) REVERT: E 64 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8806 (tp30) REVERT: E 90 ASP cc_start: 0.8546 (t0) cc_final: 0.8051 (t0) REVERT: F 42 TYR cc_start: 0.8383 (t80) cc_final: 0.8015 (t80) REVERT: F 68 ASP cc_start: 0.9203 (t0) cc_final: 0.8914 (t0) REVERT: G 59 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: G 97 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8380 (mt-10) REVERT: I 73 ASN cc_start: 0.9303 (t0) cc_final: 0.8525 (t0) REVERT: J 34 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8671 (ttpp) REVERT: J 71 GLU cc_start: 0.8981 (tp30) cc_final: 0.8700 (tp30) outliers start: 35 outliers final: 14 residues processed: 205 average time/residue: 0.7076 time to fit residues: 156.8332 Evaluate side-chains 183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 529 GLN A 567 ASN A 622 ASN C 76 GLN D 93 GLN F 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052480 restraints weight = 43815.581| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.29 r_work: 0.2687 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15728 Z= 0.142 Angle : 0.666 9.118 22547 Z= 0.374 Chirality : 0.044 0.219 2575 Planarity : 0.004 0.049 1830 Dihedral : 30.147 170.524 4434 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 3.93 % Allowed : 17.64 % Favored : 78.43 % 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: 1.80 (0.26), residues: 1087 helix: 2.64 (0.21), residues: 557 sheet: 0.54 (0.51), residues: 109 loop : -0.66 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 23 TYR 0.019 0.002 TYR A 336 PHE 0.018 0.001 PHE A 276 TRP 0.016 0.002 TRP A 471 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (15728) covalent geometry : angle 0.66580 / 0.37 (22547) hydrogen bonds : bond 0.04173 / 2.86 ( 872) hydrogen bonds : angle 3.40679 / 2.33 ( 2185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: A 620 MET cc_start: 0.8061 (mtm) cc_final: 0.7784 (ttp) REVERT: D 84 MET cc_start: 0.9149 (mmm) cc_final: 0.8651 (mmp) REVERT: E 90 ASP cc_start: 0.8486 (t0) cc_final: 0.8221 (t0) REVERT: E 104 GLN cc_start: 0.8646 (mm110) cc_final: 0.8379 (mm-40) REVERT: F 35 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8333 (mt-10) REVERT: F 42 TYR cc_start: 0.8317 (t80) cc_final: 0.7979 (t80) REVERT: F 68 ASP cc_start: 0.9198 (t0) cc_final: 0.8852 (t0) REVERT: F 101 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9083 (mm) REVERT: G 59 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6996 (pp20) REVERT: I 73 ASN cc_start: 0.9296 (t0) cc_final: 0.8567 (t0) REVERT: J 34 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8658 (ttpp) REVERT: J 71 GLU cc_start: 0.8949 (tp30) cc_final: 0.8703 (tp30) outliers start: 37 outliers final: 14 residues processed: 202 average time/residue: 0.7164 time to fit residues: 156.6341 Evaluate side-chains 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 519 GLN A 622 ASN C 76 GLN E 104 GLN J 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049860 restraints weight = 43539.708| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.27 r_work: 0.2619 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 15728 Z= 0.245 Angle : 0.698 6.743 22547 Z= 0.382 Chirality : 0.047 0.220 2575 Planarity : 0.005 0.046 1830 Dihedral : 30.561 170.445 4434 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 3.72 % Allowed : 19.13 % Favored : 77.15 % 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: 1.70 (0.25), residues: 1087 helix: 2.56 (0.21), residues: 558 sheet: 0.59 (0.50), residues: 109 loop : -0.75 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 381 TYR 0.018 0.002 TYR F 40 PHE 0.028 0.002 PHE A 630 TRP 0.016 0.002 TRP A 471 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.25 (15728) covalent geometry : angle 0.69782 / 0.38 (22547) hydrogen bonds : bond 0.05010 / 3.37 ( 872) hydrogen bonds : angle 3.38305 / 2.34 ( 2185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7882 (OUTLIER) REVERT: A 275 HIS cc_start: 0.7324 (m-70) cc_final: 0.6415 (m-70) REVERT: A 439 THR cc_start: 0.8344 (m) cc_final: 0.8071 (m) REVERT: A 620 MET cc_start: 0.8097 (mtm) cc_final: 0.7822 (ttp) REVERT: C 59 GLU cc_start: 0.8441 (pp20) cc_final: 0.8228 (pm20) REVERT: E 90 ASP cc_start: 0.8593 (t0) cc_final: 0.8184 (t0) REVERT: E 104 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8402 (mm-40) REVERT: F 35 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8726 (mm-30) REVERT: F 42 TYR cc_start: 0.8551 (t80) cc_final: 0.8162 (t80) REVERT: F 57 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8548 (mmtm) REVERT: F 101 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9022 (mm) REVERT: G 59 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: H 27 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: I 73 ASN cc_start: 0.9300 (t0) cc_final: 0.8442 (t0) REVERT: J 34 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8747 (ttpp) REVERT: J 71 GLU cc_start: 0.8994 (tp30) cc_final: 0.8722 (tp30) outliers start: 35 outliers final: 21 residues processed: 194 average time/residue: 0.6911 time to fit residues: 145.1358 Evaluate side-chains 190 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 40.0000 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN C 76 GLN I 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051037 restraints weight = 43705.873| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.30 r_work: 0.2655 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15728 Z= 0.149 Angle : 0.647 8.894 22547 Z= 0.358 Chirality : 0.044 0.220 2575 Planarity : 0.004 0.044 1830 Dihedral : 30.452 169.486 4434 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 3.29 % Allowed : 20.19 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.26), residues: 1087 helix: 2.66 (0.21), residues: 558 sheet: 0.72 (0.53), residues: 105 loop : -0.63 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 33 TYR 0.020 0.002 TYR F 40 PHE 0.009 0.001 PHE A 506 TRP 0.021 0.001 TRP A 471 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (15728) covalent geometry : angle 0.64689 / 0.36 (22547) hydrogen bonds : bond 0.03949 / 2.69 ( 872) hydrogen bonds : angle 3.22418 / 2.22 ( 2185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7966 (tp) REVERT: A 275 HIS cc_start: 0.7394 (m-70) cc_final: 0.6351 (m170) REVERT: A 423 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8805 (tp) REVERT: A 620 MET cc_start: 0.8037 (mtm) cc_final: 0.7749 (ttp) REVERT: A 639 SER cc_start: 0.9320 (m) cc_final: 0.8983 (p) REVERT: C 59 GLU cc_start: 0.8454 (pp20) cc_final: 0.8206 (pm20) REVERT: D 84 MET cc_start: 0.9146 (mmm) cc_final: 0.8773 (mmp) REVERT: E 36 LYS cc_start: 0.9491 (mmtp) cc_final: 0.9228 (mmpt) REVERT: E 90 ASP cc_start: 0.8557 (t0) cc_final: 0.8140 (t0) REVERT: E 104 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8452 (mm-40) REVERT: F 35 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8752 (mm-30) REVERT: F 42 TYR cc_start: 0.8415 (t80) cc_final: 0.8036 (t80) REVERT: F 57 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8505 (mmtm) REVERT: F 101 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9080 (mm) REVERT: G 59 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7053 (pp20) REVERT: I 73 ASN cc_start: 0.9268 (t0) cc_final: 0.8438 (t0) REVERT: J 34 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8709 (ttpp) REVERT: J 35 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8279 (mm-30) REVERT: J 71 GLU cc_start: 0.8995 (tp30) cc_final: 0.8733 (tp30) outliers start: 31 outliers final: 16 residues processed: 197 average time/residue: 0.7209 time to fit residues: 153.7269 Evaluate side-chains 191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 364 ASN A 622 ASN C 76 GLN H 27 GLN J 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.049437 restraints weight = 43290.080| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.25 r_work: 0.2614 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 15728 Z= 0.227 Angle : 0.689 9.219 22547 Z= 0.374 Chirality : 0.046 0.222 2575 Planarity : 0.005 0.072 1830 Dihedral : 30.569 170.175 4434 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 3.72 % Allowed : 20.62 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.26), residues: 1087 helix: 2.56 (0.21), residues: 559 sheet: 0.50 (0.53), residues: 100 loop : -0.68 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 33 TYR 0.024 0.002 TYR F 40 PHE 0.011 0.001 PHE B 16 TRP 0.021 0.002 TRP A 471 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (15728) covalent geometry : angle 0.68900 / 0.37 (22547) hydrogen bonds : bond 0.05044 / 3.38 ( 872) hydrogen bonds : angle 3.28055 / 2.27 ( 2185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.430 Fit side-chains REVERT: A 275 HIS cc_start: 0.7521 (m-70) cc_final: 0.6659 (m170) REVERT: A 423 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8794 (tp) REVERT: A 506 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 620 MET cc_start: 0.8001 (mtm) cc_final: 0.7680 (ttp) REVERT: A 639 SER cc_start: 0.9340 (m) cc_final: 0.9012 (p) REVERT: C 59 GLU cc_start: 0.8552 (pp20) cc_final: 0.8277 (pm20) REVERT: D 92 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8790 (ttp80) REVERT: E 90 ASP cc_start: 0.8644 (t0) cc_final: 0.8194 (t0) REVERT: E 104 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8468 (mm-40) REVERT: F 42 TYR cc_start: 0.8603 (t80) cc_final: 0.8184 (t80) REVERT: F 57 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8568 (mmtm) REVERT: F 101 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8972 (mm) REVERT: G 59 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: G 129 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8965 (tpt90) REVERT: I 73 ASN cc_start: 0.9213 (t0) cc_final: 0.8418 (t0) REVERT: J 34 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8808 (ttpp) REVERT: J 35 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8233 (mm-30) REVERT: J 71 GLU cc_start: 0.9008 (tp30) cc_final: 0.8726 (tp30) outliers start: 35 outliers final: 19 residues processed: 198 average time/residue: 0.7329 time to fit residues: 156.6866 Evaluate side-chains 190 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 29 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN A 622 ASN C 76 GLN D 25 ASN H 27 GLN I 31 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.049514 restraints weight = 43390.480| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.27 r_work: 0.2622 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15728 Z= 0.208 Angle : 0.674 10.848 22547 Z= 0.367 Chirality : 0.045 0.221 2575 Planarity : 0.004 0.042 1830 Dihedral : 30.568 170.000 4434 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 3.93 % Allowed : 21.36 % Favored : 74.71 % 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: 1.78 (0.26), residues: 1087 helix: 2.61 (0.21), residues: 559 sheet: 0.59 (0.52), residues: 105 loop : -0.66 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 33 TYR 0.023 0.002 TYR F 40 PHE 0.009 0.001 PHE B 16 TRP 0.023 0.002 TRP A 471 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (15728) covalent geometry : angle 0.67391 / 0.37 (22547) hydrogen bonds : bond 0.04343 / 2.93 ( 872) hydrogen bonds : angle 3.23767 / 2.24 ( 2185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7522 (m-70) cc_final: 0.6673 (m170) REVERT: A 423 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8772 (tp) REVERT: A 439 THR cc_start: 0.8240 (m) cc_final: 0.7958 (m) REVERT: A 639 SER cc_start: 0.9327 (m) cc_final: 0.8994 (p) REVERT: C 59 GLU cc_start: 0.8503 (pp20) cc_final: 0.8200 (pm20) REVERT: D 84 MET cc_start: 0.9145 (mmm) cc_final: 0.8785 (mmp) REVERT: D 92 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8724 (ttp80) REVERT: E 90 ASP cc_start: 0.8636 (t0) cc_final: 0.8190 (t0) REVERT: E 104 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8460 (mm-40) REVERT: F 35 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8656 (mm-30) REVERT: F 42 TYR cc_start: 0.8547 (t80) cc_final: 0.8146 (t80) REVERT: F 57 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8550 (mmtm) REVERT: F 101 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8990 (mm) REVERT: G 59 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: J 34 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8795 (ttpp) REVERT: J 35 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8276 (mm-30) REVERT: J 71 GLU cc_start: 0.9017 (tp30) cc_final: 0.8770 (tp30) outliers start: 37 outliers final: 22 residues processed: 194 average time/residue: 0.7036 time to fit residues: 147.3059 Evaluate side-chains 196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 67 optimal weight: 0.0170 chunk 132 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN C 76 GLN D 25 ASN H 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050706 restraints weight = 43561.317| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.28 r_work: 0.2655 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15728 Z= 0.135 Angle : 0.648 11.033 22547 Z= 0.357 Chirality : 0.044 0.280 2575 Planarity : 0.005 0.083 1830 Dihedral : 30.373 169.461 4434 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 2.98 % Allowed : 22.21 % Favored : 74.81 % 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: 1.85 (0.26), residues: 1087 helix: 2.65 (0.21), residues: 559 sheet: 0.55 (0.51), residues: 105 loop : -0.59 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 23 TYR 0.026 0.002 TYR F 40 PHE 0.009 0.001 PHE C 67 TRP 0.031 0.002 TRP A 471 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (15728) covalent geometry : angle 0.64763 / 0.36 (22547) hydrogen bonds : bond 0.03802 / 2.60 ( 872) hydrogen bonds : angle 3.14624 / 2.17 ( 2185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 275 HIS cc_start: 0.7514 (m-70) cc_final: 0.6582 (m170) REVERT: A 476 ASP cc_start: 0.8673 (m-30) cc_final: 0.7974 (p0) REVERT: A 620 MET cc_start: 0.7826 (mtt) cc_final: 0.7520 (ttp) REVERT: A 639 SER cc_start: 0.9295 (m) cc_final: 0.8947 (p) REVERT: C 59 GLU cc_start: 0.8475 (pp20) cc_final: 0.8128 (pm20) REVERT: D 84 MET cc_start: 0.9107 (mmm) cc_final: 0.8785 (mmp) REVERT: D 92 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8758 (ttp80) REVERT: E 90 ASP cc_start: 0.8628 (t0) cc_final: 0.8204 (t0) REVERT: F 42 TYR cc_start: 0.8473 (t80) cc_final: 0.8073 (t80) REVERT: F 57 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8535 (mmtm) REVERT: F 101 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9024 (mm) REVERT: G 59 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: J 34 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8796 (ttpp) REVERT: J 71 GLU cc_start: 0.9020 (tp30) cc_final: 0.8751 (tp30) outliers start: 28 outliers final: 18 residues processed: 194 average time/residue: 0.6746 time to fit residues: 140.9796 Evaluate side-chains 192 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN A 622 ASN C 76 GLN E 104 GLN H 27 GLN J 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.049669 restraints weight = 44127.407| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.28 r_work: 0.2624 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15728 Z= 0.216 Angle : 0.672 13.463 22547 Z= 0.366 Chirality : 0.045 0.223 2575 Planarity : 0.004 0.039 1830 Dihedral : 30.419 169.755 4434 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 22.21 % Favored : 74.71 % 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: 1.83 (0.26), residues: 1087 helix: 2.66 (0.21), residues: 559 sheet: 0.47 (0.51), residues: 105 loop : -0.62 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 29 TYR 0.028 0.002 TYR F 40 PHE 0.010 0.001 PHE B 16 TRP 0.026 0.002 TRP A 471 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (15728) covalent geometry : angle 0.67166 / 0.37 (22547) hydrogen bonds : bond 0.04255 / 2.87 ( 872) hydrogen bonds : angle 3.19854 / 2.21 ( 2185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7947 (tp) REVERT: A 275 HIS cc_start: 0.7579 (m-70) cc_final: 0.6683 (m170) REVERT: A 423 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 439 THR cc_start: 0.8225 (m) cc_final: 0.7949 (m) REVERT: A 476 ASP cc_start: 0.8717 (m-30) cc_final: 0.8012 (p0) REVERT: A 620 MET cc_start: 0.7841 (mtt) cc_final: 0.7522 (ttp) REVERT: A 639 SER cc_start: 0.9305 (m) cc_final: 0.8967 (p) REVERT: C 59 GLU cc_start: 0.8542 (pp20) cc_final: 0.8173 (pm20) REVERT: D 84 MET cc_start: 0.9168 (mmm) cc_final: 0.8825 (mmp) REVERT: D 92 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8746 (ttp80) REVERT: E 90 ASP cc_start: 0.8673 (t0) cc_final: 0.8221 (t0) REVERT: F 42 TYR cc_start: 0.8580 (t80) cc_final: 0.8155 (t80) REVERT: F 101 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9005 (mm) REVERT: G 59 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7250 (pp20) REVERT: J 34 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8776 (ttpp) REVERT: J 71 GLU cc_start: 0.9042 (tp30) cc_final: 0.8770 (tp30) outliers start: 29 outliers final: 21 residues processed: 181 average time/residue: 0.7202 time to fit residues: 140.7855 Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 121 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN A 622 ASN C 76 GLN H 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050344 restraints weight = 43534.093| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.27 r_work: 0.2642 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15728 Z= 0.158 Angle : 0.656 14.169 22547 Z= 0.361 Chirality : 0.044 0.220 2575 Planarity : 0.005 0.069 1830 Dihedral : 30.375 169.635 4434 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 2.87 % Allowed : 22.64 % Favored : 74.50 % 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: 1.83 (0.26), residues: 1087 helix: 2.68 (0.21), residues: 559 sheet: 0.45 (0.51), residues: 105 loop : -0.64 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 282 TYR 0.028 0.002 TYR F 40 PHE 0.008 0.001 PHE C 67 TRP 0.029 0.002 TRP A 471 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (15728) covalent geometry : angle 0.65621 / 0.36 (22547) hydrogen bonds : bond 0.03944 / 2.67 ( 872) hydrogen bonds : angle 3.15167 / 2.17 ( 2185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7993 (tp) REVERT: A 275 HIS cc_start: 0.7580 (m-70) cc_final: 0.6690 (m170) REVERT: A 439 THR cc_start: 0.8201 (m) cc_final: 0.7926 (m) REVERT: A 476 ASP cc_start: 0.8697 (m-30) cc_final: 0.7999 (p0) REVERT: A 620 MET cc_start: 0.7748 (mtt) cc_final: 0.7417 (ttp) REVERT: A 639 SER cc_start: 0.9301 (m) cc_final: 0.8948 (p) REVERT: C 59 GLU cc_start: 0.8536 (pp20) cc_final: 0.8181 (pm20) REVERT: D 92 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8733 (ttp80) REVERT: E 90 ASP cc_start: 0.8655 (t0) cc_final: 0.8232 (t0) REVERT: F 42 TYR cc_start: 0.8529 (t80) cc_final: 0.8115 (t80) REVERT: F 101 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8990 (mm) REVERT: G 59 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: J 34 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8805 (ttpp) REVERT: J 71 GLU cc_start: 0.9023 (tp30) cc_final: 0.8753 (tp30) outliers start: 27 outliers final: 19 residues processed: 184 average time/residue: 0.7151 time to fit residues: 142.0429 Evaluate side-chains 188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN C 76 GLN H 27 GLN H 93 GLN I 24 GLN J 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.046936 restraints weight = 43567.403| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.26 r_work: 0.2550 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.148 15728 Z= 0.401 Angle : 0.821 14.392 22547 Z= 0.428 Chirality : 0.052 0.227 2575 Planarity : 0.006 0.054 1830 Dihedral : 30.889 172.092 4434 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 2.87 % Allowed : 22.85 % Favored : 74.28 % 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: 1.38 (0.25), residues: 1087 helix: 2.31 (0.21), residues: 560 sheet: 0.25 (0.48), residues: 110 loop : -0.87 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 33 TYR 0.035 0.003 TYR F 40 PHE 0.035 0.002 PHE B 16 TRP 0.023 0.003 TRP A 471 HIS 0.007 0.002 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.40 (15728) covalent geometry : angle 0.82125 / 0.43 (22547) hydrogen bonds : bond 0.06406 / 4.30 ( 872) hydrogen bonds : angle 3.49372 / 2.42 ( 2185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4676.52 seconds wall clock time: 80 minutes 13.45 seconds (4813.45 seconds total)