Starting phenix.real_space_refine on Fri Jul 3 13:56:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8siy_40522/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.cif" model { file = "/net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8siy_40522/07_2026/8siy_40522.cif" } 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-dev-6108/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: 3.04, per 1000 atoms: 0.20 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: 1.25 Conformation dependent library (CDL) restraints added in 502.8 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: 3.41 Time building geometry restraints manager: 1.69 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: 21485 1.78 - 3.56: 1003 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: 2.100 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.910 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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= 0.586 Angle : 0.776 8.890 22547 Z= 0.639 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 0.77613 / 0.64 (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 : 0.372 Fit side-chains REVERT: I 73 ASN cc_start: 0.8454 (t0) cc_final: 0.8202 (t0) outliers start: 13 outliers final: 3 residues processed: 278 average time/residue: 0.6634 time to fit residues: 199.0484 Evaluate side-chains 173 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 G 76 GLN G 108 ASN I 24 GLN 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 = 0.3532 r_free = 0.3532 target = 0.080024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051395 restraints weight = 43251.308| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.27 r_work: 0.2659 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15728 Z= 0.211 Angle : 0.708 8.927 22547 Z= 0.400 Chirality : 0.047 0.222 2575 Planarity : 0.005 0.055 1830 Dihedral : 30.098 172.206 4438 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.83 % Allowed : 17.43 % Favored : 78.75 % 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: 1.68 (0.25), residues: 1087 helix: 2.49 (0.21), residues: 557 sheet: 0.37 (0.48), residues: 118 loop : -0.62 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 381 TYR 0.020 0.002 TYR A 632 PHE 0.014 0.001 PHE A 630 TRP 0.015 0.002 TRP A 471 HIS 0.011 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (15728) covalent geometry : angle 0.70809 / 0.40 (22547) hydrogen bonds : bond 0.04935 / 3.39 ( 872) hydrogen bonds : angle 3.68861 / 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 219 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7235 (m-70) cc_final: 0.6900 (m-70) REVERT: A 567 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8066 (t0) REVERT: A 620 MET cc_start: 0.8041 (mtm) cc_final: 0.7748 (ttp) REVERT: E 64 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8784 (tp30) REVERT: E 90 ASP cc_start: 0.8554 (t0) cc_final: 0.8072 (t0) REVERT: F 68 ASP cc_start: 0.9199 (t0) cc_final: 0.8918 (t0) REVERT: G 59 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: G 97 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8358 (mt-10) REVERT: I 24 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8684 (mm-40) REVERT: I 73 ASN cc_start: 0.9301 (t0) cc_final: 0.8511 (t0) REVERT: J 34 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8636 (ttpp) REVERT: J 71 GLU cc_start: 0.8974 (tp30) cc_final: 0.8692 (tp30) REVERT: J 93 GLU cc_start: 0.8955 (mp0) cc_final: 0.8741 (mp0) outliers start: 36 outliers final: 14 residues processed: 203 average time/residue: 0.6907 time to fit residues: 151.3800 Evaluate side-chains 183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 I residue 24 GLN 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: 8.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.080856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052476 restraints weight = 43701.206| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.28 r_work: 0.2688 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15728 Z= 0.142 Angle : 0.653 8.859 22547 Z= 0.371 Chirality : 0.044 0.205 2575 Planarity : 0.004 0.049 1830 Dihedral : 30.200 170.190 4434 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 3.72 % Allowed : 17.53 % Favored : 78.75 % 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: 2.66 (0.21), residues: 557 sheet: 0.47 (0.51), residues: 108 loop : -0.67 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 23 TYR 0.019 0.002 TYR A 336 PHE 0.017 0.001 PHE A 630 TRP 0.016 0.001 TRP A 471 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (15728) covalent geometry : angle 0.65251 / 0.37 (22547) hydrogen bonds : bond 0.04186 / 2.87 ( 872) hydrogen bonds : angle 3.42853 / 2.34 ( 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 218 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: A 342 GLU cc_start: 0.7890 (mp0) cc_final: 0.7531 (mp0) REVERT: A 620 MET cc_start: 0.8026 (mtm) cc_final: 0.7745 (ttp) REVERT: D 84 MET cc_start: 0.9131 (mmm) cc_final: 0.8647 (mmp) REVERT: E 90 ASP cc_start: 0.8442 (t0) cc_final: 0.8178 (t0) REVERT: E 104 GLN cc_start: 0.8632 (mm110) cc_final: 0.8364 (mm-40) REVERT: F 35 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8269 (mt-10) REVERT: F 68 ASP cc_start: 0.9182 (t0) cc_final: 0.8838 (t0) REVERT: F 101 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9044 (mm) REVERT: G 59 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: I 73 ASN cc_start: 0.9293 (t0) cc_final: 0.8488 (t0) REVERT: I 75 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9251 (mttm) REVERT: J 34 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8649 (ttpp) REVERT: J 71 GLU cc_start: 0.8944 (tp30) cc_final: 0.8689 (tp30) outliers start: 35 outliers final: 13 residues processed: 201 average time/residue: 0.6829 time to fit residues: 148.5776 Evaluate side-chains 186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 I residue 75 LYS 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: 0.7980 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 622 ASN C 76 GLN E 104 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 = 0.3523 r_free = 0.3523 target = 0.079409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.050680 restraints weight = 43467.592| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.28 r_work: 0.2643 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15728 Z= 0.198 Angle : 0.662 8.601 22547 Z= 0.369 Chirality : 0.045 0.202 2575 Planarity : 0.005 0.052 1830 Dihedral : 30.525 169.417 4434 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 3.40 % Allowed : 19.34 % Favored : 77.26 % 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: 1.79 (0.26), residues: 1087 helix: 2.66 (0.21), residues: 558 sheet: 0.62 (0.51), residues: 109 loop : -0.76 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 33 TYR 0.020 0.002 TYR A 336 PHE 0.031 0.001 PHE A 630 TRP 0.015 0.002 TRP A 471 HIS 0.010 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (15728) covalent geometry : angle 0.66205 / 0.37 (22547) hydrogen bonds : bond 0.04607 / 3.11 ( 872) hydrogen bonds : angle 3.31735 / 2.28 ( 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 207 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7281 (m-70) cc_final: 0.6439 (m-70) REVERT: A 439 THR cc_start: 0.8309 (m) cc_final: 0.8042 (m) REVERT: A 620 MET cc_start: 0.8039 (mtm) cc_final: 0.7763 (ttp) REVERT: C 59 GLU cc_start: 0.8404 (pp20) cc_final: 0.8189 (pm20) REVERT: E 90 ASP cc_start: 0.8554 (t0) cc_final: 0.8187 (t0) REVERT: E 104 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8415 (mm-40) REVERT: F 101 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9017 (mm) REVERT: G 59 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7056 (pp20) REVERT: H 27 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: I 73 ASN cc_start: 0.9280 (t0) cc_final: 0.8469 (t0) REVERT: J 34 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8689 (ttpp) REVERT: J 71 GLU cc_start: 0.8978 (tp30) cc_final: 0.8706 (tp30) outliers start: 32 outliers final: 19 residues processed: 191 average time/residue: 0.7270 time to fit residues: 149.9056 Evaluate side-chains 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 34 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 27 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 50.0000 chunk 29 optimal weight: 0.0060 chunk 60 optimal weight: 7.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN C 76 GLN D 27 GLN I 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050489 restraints weight = 43669.685| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.27 r_work: 0.2646 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15728 Z= 0.185 Angle : 0.638 8.062 22547 Z= 0.356 Chirality : 0.044 0.203 2575 Planarity : 0.004 0.042 1830 Dihedral : 30.570 168.721 4434 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 3.08 % Allowed : 20.72 % Favored : 76.20 % 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: 1.87 (0.26), residues: 1087 helix: 2.72 (0.21), residues: 558 sheet: 0.61 (0.53), residues: 105 loop : -0.69 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 86 TYR 0.020 0.002 TYR F 40 PHE 0.017 0.001 PHE A 506 TRP 0.021 0.002 TRP A 471 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (15728) covalent geometry : angle 0.63773 / 0.36 (22547) hydrogen bonds : bond 0.04072 / 2.76 ( 872) hydrogen bonds : angle 3.23354 / 2.23 ( 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 205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7651 (m-70) cc_final: 0.6844 (m-70) REVERT: A 423 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8831 (tp) REVERT: A 439 THR cc_start: 0.8251 (m) cc_final: 0.7970 (m) REVERT: A 620 MET cc_start: 0.8050 (mtm) cc_final: 0.7782 (ttp) REVERT: A 639 SER cc_start: 0.9323 (m) cc_final: 0.8990 (p) REVERT: C 59 GLU cc_start: 0.8496 (pp20) cc_final: 0.8253 (pm20) REVERT: D 84 MET cc_start: 0.9127 (mmm) cc_final: 0.8783 (mmp) REVERT: E 90 ASP cc_start: 0.8607 (t0) cc_final: 0.8173 (t0) REVERT: E 104 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8485 (mm-40) REVERT: F 35 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8610 (mm-30) REVERT: F 57 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8554 (mmtm) REVERT: F 101 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9097 (mm) REVERT: G 59 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7062 (pp20) REVERT: I 73 ASN cc_start: 0.9230 (t0) cc_final: 0.8403 (t0) REVERT: J 34 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8743 (ttpp) REVERT: J 71 GLU cc_start: 0.9012 (tp30) cc_final: 0.8756 (tp30) outliers start: 29 outliers final: 16 residues processed: 193 average time/residue: 0.7279 time to fit residues: 151.7263 Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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 101 THR 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: 2.9990 chunk 124 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN A 529 GLN A 622 ASN C 76 GLN D 27 GLN H 27 GLN J 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050424 restraints weight = 43322.059| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.26 r_work: 0.2646 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15728 Z= 0.182 Angle : 0.638 9.222 22547 Z= 0.356 Chirality : 0.044 0.203 2575 Planarity : 0.004 0.055 1830 Dihedral : 30.515 168.858 4434 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 3.51 % Allowed : 20.62 % Favored : 75.88 % 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: 2.67 (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 0.000 ARG F 33 TYR 0.022 0.002 TYR F 40 PHE 0.009 0.001 PHE G 67 TRP 0.020 0.001 TRP A 471 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (15728) covalent geometry : angle 0.63778 / 0.36 (22547) hydrogen bonds : bond 0.04142 / 2.80 ( 872) hydrogen bonds : angle 3.21624 / 2.22 ( 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 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7542 (m-70) cc_final: 0.6784 (m170) REVERT: A 423 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8779 (tp) REVERT: A 439 THR cc_start: 0.8264 (m) cc_final: 0.7987 (m) REVERT: A 476 ASP cc_start: 0.8671 (m-30) cc_final: 0.7933 (p0) REVERT: A 506 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 620 MET cc_start: 0.8020 (mtm) cc_final: 0.7699 (ttp) REVERT: A 639 SER cc_start: 0.9310 (m) cc_final: 0.8979 (p) REVERT: C 59 GLU cc_start: 0.8531 (pp20) cc_final: 0.8273 (pm20) REVERT: E 90 ASP cc_start: 0.8625 (t0) cc_final: 0.8178 (t0) REVERT: E 104 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8498 (mm110) REVERT: F 57 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8553 (mmtm) REVERT: F 101 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9028 (mm) REVERT: G 59 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: I 73 ASN cc_start: 0.9219 (t0) cc_final: 0.8417 (t0) REVERT: J 71 GLU cc_start: 0.9027 (tp30) cc_final: 0.8765 (tp30) outliers start: 33 outliers final: 16 residues processed: 195 average time/residue: 0.7145 time to fit residues: 150.1210 Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 101 THR Chi-restraints excluded: chain I residue 114 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: 0.0980 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN A 408 HIS 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 = 0.3512 r_free = 0.3512 target = 0.078659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.050099 restraints weight = 43367.106| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.26 r_work: 0.2638 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15728 Z= 0.194 Angle : 0.654 11.083 22547 Z= 0.361 Chirality : 0.044 0.203 2575 Planarity : 0.004 0.039 1830 Dihedral : 30.532 168.878 4434 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.72 % Allowed : 21.36 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.26), residues: 1087 helix: 2.68 (0.21), residues: 559 sheet: 0.43 (0.53), residues: 100 loop : -0.70 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 86 TYR 0.023 0.002 TYR F 40 PHE 0.008 0.001 PHE B 16 TRP 0.024 0.002 TRP A 471 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (15728) covalent geometry : angle 0.65354 / 0.36 (22547) hydrogen bonds : bond 0.04142 / 2.80 ( 872) hydrogen bonds : angle 3.20396 / 2.21 ( 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 206 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7615 (m-70) cc_final: 0.6870 (m170) REVERT: A 423 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8743 (tp) REVERT: A 439 THR cc_start: 0.8257 (m) cc_final: 0.7969 (m) REVERT: A 476 ASP cc_start: 0.8684 (m-30) cc_final: 0.7966 (p0) REVERT: A 620 MET cc_start: 0.8052 (mtm) cc_final: 0.7766 (ttp) REVERT: A 639 SER cc_start: 0.9314 (m) cc_final: 0.8988 (p) REVERT: C 59 GLU cc_start: 0.8475 (pp20) cc_final: 0.8186 (pm20) REVERT: D 84 MET cc_start: 0.9147 (mmm) cc_final: 0.8843 (mmp) REVERT: E 90 ASP cc_start: 0.8625 (t0) cc_final: 0.8202 (t0) REVERT: E 104 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8485 (mm110) REVERT: F 35 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8529 (mm-30) REVERT: F 57 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8549 (mmtm) REVERT: F 101 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9073 (mm) REVERT: G 59 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: J 71 GLU cc_start: 0.9025 (tp30) cc_final: 0.8777 (tp30) outliers start: 35 outliers final: 22 residues processed: 190 average time/residue: 0.7248 time to fit residues: 148.3439 Evaluate side-chains 195 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 ASP 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 642 VAL Chi-restraints excluded: chain C residue 115 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 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 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: 0.6980 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN C 76 GLN H 27 GLN I 31 HIS J 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.049595 restraints weight = 43711.291| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.28 r_work: 0.2623 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 15728 Z= 0.217 Angle : 0.666 11.468 22547 Z= 0.366 Chirality : 0.045 0.204 2575 Planarity : 0.005 0.064 1830 Dihedral : 30.561 169.173 4434 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 3.40 % Allowed : 21.36 % Favored : 75.24 % 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: 1.77 (0.26), residues: 1087 helix: 2.66 (0.21), residues: 559 sheet: 0.29 (0.52), residues: 100 loop : -0.67 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 23 TYR 0.026 0.002 TYR F 40 PHE 0.010 0.001 PHE B 16 TRP 0.025 0.002 TRP A 471 HIS 0.006 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (15728) covalent geometry : angle 0.66608 / 0.37 (22547) hydrogen bonds : bond 0.04326 / 2.92 ( 872) hydrogen bonds : angle 3.23213 / 2.23 ( 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 199 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.7650 (m-70) cc_final: 0.6925 (m170) REVERT: A 336 TYR cc_start: 0.7897 (t80) cc_final: 0.7569 (t80) REVERT: A 476 ASP cc_start: 0.8671 (m-30) cc_final: 0.7996 (p0) REVERT: A 620 MET cc_start: 0.7984 (mtm) cc_final: 0.7677 (ttp) REVERT: A 639 SER cc_start: 0.9318 (m) cc_final: 0.8991 (p) REVERT: C 59 GLU cc_start: 0.8525 (pp20) cc_final: 0.8184 (pm20) REVERT: D 84 MET cc_start: 0.9179 (mmm) cc_final: 0.8855 (mmp) REVERT: E 90 ASP cc_start: 0.8656 (t0) cc_final: 0.8211 (t0) REVERT: E 104 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8485 (mm-40) REVERT: F 57 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8563 (mmtm) REVERT: F 101 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9035 (mm) REVERT: G 59 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: J 71 GLU cc_start: 0.9032 (tp30) cc_final: 0.8787 (tp30) outliers start: 32 outliers final: 19 residues processed: 185 average time/residue: 0.7503 time to fit residues: 149.7757 Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 101 THR Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN A 408 HIS 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 = 0.3500 r_free = 0.3500 target = 0.077975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.049449 restraints weight = 44226.102| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.29 r_work: 0.2622 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15728 Z= 0.209 Angle : 0.669 14.790 22547 Z= 0.365 Chirality : 0.045 0.204 2575 Planarity : 0.005 0.073 1830 Dihedral : 30.569 169.430 4434 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 3.19 % Allowed : 22.00 % 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: 1.82 (0.26), residues: 1087 helix: 2.69 (0.21), residues: 559 sheet: 0.33 (0.50), residues: 105 loop : -0.64 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 23 TYR 0.025 0.002 TYR F 40 PHE 0.018 0.001 PHE A 506 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 0.00437 / 0.21 (15728) covalent geometry : angle 0.66882 / 0.37 (22547) hydrogen bonds : bond 0.04238 / 2.86 ( 872) hydrogen bonds : angle 3.23469 / 2.25 ( 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 199 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7883 (tp) REVERT: A 275 HIS cc_start: 0.7693 (m-70) cc_final: 0.6880 (m170) REVERT: A 378 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8546 (tp) REVERT: A 476 ASP cc_start: 0.8718 (m-30) cc_final: 0.8030 (p0) REVERT: A 639 SER cc_start: 0.9317 (m) cc_final: 0.8992 (p) REVERT: C 59 GLU cc_start: 0.8549 (pp20) cc_final: 0.8175 (pm20) REVERT: E 90 ASP cc_start: 0.8667 (t0) cc_final: 0.8225 (t0) REVERT: E 104 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8498 (mm-40) REVERT: F 35 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8671 (mm-30) REVERT: F 101 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9026 (mm) REVERT: G 59 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7267 (pp20) REVERT: J 34 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8746 (tttt) REVERT: J 71 GLU cc_start: 0.9044 (tp30) cc_final: 0.8803 (tp30) outliers start: 30 outliers final: 21 residues processed: 186 average time/residue: 0.7342 time to fit residues: 147.5882 Evaluate side-chains 189 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE 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 C residue 115 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 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 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 121 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN A 622 ASN C 68 GLN 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 = 0.3529 r_free = 0.3529 target = 0.079497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051098 restraints weight = 43599.587| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.27 r_work: 0.2669 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15728 Z= 0.133 Angle : 0.627 12.785 22547 Z= 0.350 Chirality : 0.043 0.218 2575 Planarity : 0.005 0.081 1830 Dihedral : 30.316 168.557 4434 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 2.34 % Allowed : 23.70 % Favored : 73.96 % 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: 1.92 (0.26), residues: 1087 helix: 2.75 (0.22), residues: 559 sheet: 0.36 (0.50), residues: 105 loop : -0.55 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 33 TYR 0.024 0.002 TYR F 40 PHE 0.030 0.001 PHE B 16 TRP 0.032 0.002 TRP A 471 HIS 0.005 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (15728) covalent geometry : angle 0.62668 / 0.35 (22547) hydrogen bonds : bond 0.03689 / 2.52 ( 872) hydrogen bonds : angle 3.13959 / 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 206 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 275 HIS cc_start: 0.7665 (m-70) cc_final: 0.6881 (m170) REVERT: A 378 LEU cc_start: 0.9030 (mm) cc_final: 0.8543 (tp) REVERT: A 476 ASP cc_start: 0.8685 (m-30) cc_final: 0.8004 (p0) REVERT: A 620 MET cc_start: 0.7668 (mtt) cc_final: 0.7375 (tpp) REVERT: A 639 SER cc_start: 0.9291 (m) cc_final: 0.8937 (p) REVERT: C 59 GLU cc_start: 0.8521 (pp20) cc_final: 0.8135 (pm20) REVERT: E 90 ASP cc_start: 0.8619 (t0) cc_final: 0.8191 (t0) REVERT: F 101 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9072 (mm) REVERT: G 59 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: J 34 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8719 (tttt) REVERT: J 71 GLU cc_start: 0.9026 (tp30) cc_final: 0.8763 (tp30) outliers start: 22 outliers final: 17 residues processed: 197 average time/residue: 0.7729 time to fit residues: 164.3977 Evaluate side-chains 189 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 642 VAL Chi-restraints excluded: chain C residue 115 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 ASN C 68 GLN C 76 GLN D 93 GLN E 104 GLN H 27 GLN H 93 GLN J 47 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.050958 restraints weight = 43522.768| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.27 r_work: 0.2665 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.455 15728 Z= 0.332 Angle : 0.941 59.138 22547 Z= 0.514 Chirality : 0.057 1.796 2575 Planarity : 0.005 0.098 1830 Dihedral : 30.303 168.561 4434 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.23 % Allowed : 23.80 % Favored : 73.96 % Cbeta Deviations : 0.10 % 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: 1.88 (0.26), residues: 1087 helix: 2.70 (0.21), residues: 559 sheet: 0.35 (0.50), residues: 105 loop : -0.55 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 23 TYR 0.023 0.002 TYR F 40 PHE 0.026 0.001 PHE B 16 TRP 0.028 0.001 TRP A 471 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.33 (15728) covalent geometry : angle 0.94122 / 0.51 (22547) hydrogen bonds : bond 0.03785 / 2.58 ( 872) hydrogen bonds : angle 3.13795 / 2.17 ( 2185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4876.22 seconds wall clock time: 83 minutes 54.24 seconds (5034.24 seconds total)