Starting phenix.real_space_refine on Sat Jun 14 11:42:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcc_37099/06_2025/8kcc_37099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcc_37099/06_2025/8kcc_37099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kcc_37099/06_2025/8kcc_37099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcc_37099/06_2025/8kcc_37099.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcc_37099/06_2025/8kcc_37099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcc_37099/06_2025/8kcc_37099.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.003 sd= 0.055 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: 7 Type Number sf(0) Gaussians P 302 5.49 5 S 34 5.16 5 Be 1 3.05 5 C 9342 2.51 5 N 2986 2.21 5 O 3603 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16271 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "C" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 719 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3053 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3097 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4088 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 487} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.00, per 1000 atoms: 0.55 Number of scatterers: 16271 At special positions: 0 Unit cell: (134.734, 100.05, 142.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 P 302 15.00 F 3 9.00 O 3603 8.00 N 2986 7.00 C 9342 6.00 Be 1 4.00 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: 3.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 65.4% alpha, 6.9% beta 60 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.557A pdb=" N ILE A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 82 removed outlier: 4.416A pdb=" N VAL A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.689A pdb=" N ILE B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 82 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 75 through 104 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 124 through 144 Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 75 through 104 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 144 Processing helix chain 'E' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.528A pdb=" N ILE G 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.732A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 48 through 76 removed outlier: 4.479A pdb=" N GLU H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.531A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 Processing helix chain 'K' and resid 203 through 220 Processing helix chain 'K' and resid 232 through 247 removed outlier: 3.885A pdb=" N GLN K 236 " --> pdb=" O GLY K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 272 removed outlier: 4.188A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 Processing helix chain 'K' and resid 310 through 318 Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.591A pdb=" N ARG K 347 " --> pdb=" O CYS K 343 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 380 removed outlier: 3.932A pdb=" N SER K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 375 " --> pdb=" O GLU K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 394 removed outlier: 3.739A pdb=" N PHE K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 424 Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 472 Processing helix chain 'K' and resid 489 through 498 Processing helix chain 'K' and resid 499 through 509 removed outlier: 3.905A pdb=" N LEU K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 523 removed outlier: 4.401A pdb=" N CYS K 523 " --> pdb=" O ILE K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 540 Processing helix chain 'K' and resid 549 through 564 removed outlier: 3.599A pdb=" N LEU K 553 " --> pdb=" O TRP K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 623 through 632 removed outlier: 3.749A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 671 removed outlier: 4.001A pdb=" N LEU K 668 " --> pdb=" O SER K 664 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 669 " --> pdb=" O LYS K 665 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 711 removed outlier: 3.595A pdb=" N THR K 711 " --> pdb=" O LYS K 707 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 723 removed outlier: 3.791A pdb=" N ASP K 723 " --> pdb=" O ASP K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.970A pdb=" N ARG A 51 " --> pdb=" O ILE D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 52 removed outlier: 7.245A pdb=" N ARG B 51 " --> pdb=" O ILE C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.934A pdb=" N THR B 110 " --> pdb=" O TYR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.144A pdb=" N ARG E 83 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'F' and resid 83 through 84 removed outlier: 7.331A pdb=" N ARG F 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'K' and resid 224 through 225 removed outlier: 7.153A pdb=" N ILE K 224 " --> pdb=" O LEU K 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N TRP K 327 " --> pdb=" O ASP K 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU K 360 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE K 332 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.036A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER K 599 " --> pdb=" O CYS K 568 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE K 570 " --> pdb=" O SER K 599 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL K 543 " --> pdb=" O PHE K 596 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU K 598 " --> pdb=" O VAL K 543 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE K 545 " --> pdb=" O LEU K 598 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 4.59 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: 2974 1.33 - 1.45: 5348 1.45 - 1.57: 8200 1.57 - 1.69: 602 1.69 - 1.82: 57 Bond restraints: 17181 Sorted by residual: bond pdb=" C1' ADP K 801 " pdb=" C2' ADP K 801 " ideal model delta sigma weight residual 1.524 1.307 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1' ADP K 801 " pdb=" O4' ADP K 801 " ideal model delta sigma weight residual 1.426 1.628 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C4' ADP K 801 " pdb=" O4' ADP K 801 " ideal model delta sigma weight residual 1.426 1.277 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C4 ADP K 801 " pdb=" C5 ADP K 801 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" F2 BEF K 802 " pdb="BE BEF K 802 " ideal model delta sigma weight residual 1.476 1.366 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 17176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 24363 2.55 - 5.11: 91 5.11 - 7.66: 11 7.66 - 10.21: 3 10.21 - 12.77: 9 Bond angle restraints: 24477 Sorted by residual: angle pdb=" N ARG H 17 " pdb=" CA ARG H 17 " pdb=" C ARG H 17 " ideal model delta sigma weight residual 109.52 96.75 12.77 1.55e+00 4.16e-01 6.79e+01 angle pdb=" N HIS H 18 " pdb=" CA HIS H 18 " pdb=" C HIS H 18 " ideal model delta sigma weight residual 110.24 99.80 10.44 1.47e+00 4.63e-01 5.05e+01 angle pdb=" N ARG H 19 " pdb=" CA ARG H 19 " pdb=" C ARG H 19 " ideal model delta sigma weight residual 109.85 119.37 -9.52 1.58e+00 4.01e-01 3.63e+01 angle pdb=" CA GLU D 91 " pdb=" CB GLU D 91 " pdb=" CG GLU D 91 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 ... (remaining 24472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.24: 7879 30.24 - 60.49: 1632 60.49 - 90.73: 56 90.73 - 120.98: 1 120.98 - 151.22: 3 Dihedral angle restraints: 9571 sinusoidal: 5912 harmonic: 3659 Sorted by residual: dihedral pdb=" C4' ADP K 801 " pdb=" C5' ADP K 801 " pdb=" O5' ADP K 801 " pdb=" PA ADP K 801 " ideal model delta sinusoidal sigma weight residual 180.00 77.08 102.92 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" CA GLN K 366 " pdb=" C GLN K 366 " pdb=" N ASN K 367 " pdb=" CA ASN K 367 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 68.78 151.22 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2424 0.046 - 0.092: 279 0.092 - 0.139: 67 0.139 - 0.185: 2 0.185 - 0.231: 4 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA ARG H 19 " pdb=" N ARG H 19 " pdb=" C ARG H 19 " pdb=" CB ARG H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG H 17 " pdb=" N ARG H 17 " pdb=" C ARG H 17 " pdb=" CB ARG H 17 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASP H 24 " pdb=" N ASP H 24 " pdb=" C ASP H 24 " pdb=" CB ASP H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2773 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 652 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" CD GLN K 652 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN K 652 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN K 652 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " -0.021 2.00e-02 2.50e+03 9.24e-03 2.56e+00 pdb=" N9 DG I 131 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 94 " -0.017 2.00e-02 2.50e+03 8.97e-03 2.21e+00 pdb=" N9 DA I 94 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 94 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 94 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 94 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 94 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 94 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1295 2.74 - 3.28: 15815 3.28 - 3.82: 31079 3.82 - 4.36: 35745 4.36 - 4.90: 53697 Nonbonded interactions: 137631 Sorted by model distance: nonbonded pdb=" OG SER K 386 " pdb=" OD1 ASP K 388 " model vdw 2.199 3.040 nonbonded pdb=" O LEU C 93 " pdb=" OG SER C 97 " model vdw 2.218 3.040 nonbonded pdb=" O LEU D 93 " pdb=" OG SER D 97 " model vdw 2.219 3.040 nonbonded pdb=" O2 DT I 60 " pdb=" N2 DG J 92 " model vdw 2.221 3.120 nonbonded pdb=" O2 DT I 49 " pdb=" N2 DG J 103 " model vdw 2.225 3.120 ... (remaining 137626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 24 through 125) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 23 through 102) } 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: 1.050 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 40.990 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 17181 Z= 0.220 Angle : 0.550 12.768 24477 Z= 0.323 Chirality : 0.033 0.231 2776 Planarity : 0.003 0.032 2050 Dihedral : 25.142 151.222 7207 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.20 % Allowed : 1.75 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1244 helix: 0.77 (0.17), residues: 798 sheet: -1.70 (0.56), residues: 66 loop : -1.34 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 212 HIS 0.010 0.001 HIS K 670 PHE 0.012 0.001 PHE K 459 TYR 0.008 0.001 TYR B 66 ARG 0.003 0.000 ARG H 17 Details of bonding type rmsd hydrogen bonds : bond 0.17466 ( 735) hydrogen bonds : angle 6.49654 ( 2045) covalent geometry : bond 0.00433 (17181) covalent geometry : angle 0.55008 (24477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9468 (tttt) cc_final: 0.8939 (tttm) REVERT: A 70 GLU cc_start: 0.8277 (tp30) cc_final: 0.7851 (tp30) REVERT: A 84 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7770 (mmmt) REVERT: A 99 ASP cc_start: 0.8687 (t70) cc_final: 0.8168 (t0) REVERT: A 101 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8561 (mm-30) REVERT: B 26 LYS cc_start: 0.9205 (mttt) cc_final: 0.8962 (mtmm) REVERT: B 47 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8229 (mtp180) REVERT: B 70 GLU cc_start: 0.8309 (tp30) cc_final: 0.7896 (tp30) REVERT: B 73 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7875 (tp30) REVERT: B 81 ASP cc_start: 0.8988 (m-30) cc_final: 0.8756 (m-30) REVERT: B 99 ASP cc_start: 0.8610 (t0) cc_final: 0.8200 (t0) REVERT: C 52 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (tppt) REVERT: C 71 ASP cc_start: 0.8704 (p0) cc_final: 0.8341 (p0) REVERT: C 88 ASP cc_start: 0.8141 (t0) cc_final: 0.7867 (t0) REVERT: C 113 GLU cc_start: 0.8409 (mp0) cc_final: 0.8092 (mp0) REVERT: D 79 MET cc_start: 0.8647 (tpp) cc_final: 0.8363 (tpp) REVERT: D 84 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9357 (m) REVERT: D 88 ASP cc_start: 0.8536 (t0) cc_final: 0.8011 (t0) REVERT: D 96 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 113 GLU cc_start: 0.8135 (mp0) cc_final: 0.7753 (mp0) REVERT: F 50 GLU cc_start: 0.8957 (tt0) cc_final: 0.8652 (tt0) REVERT: F 125 GLN cc_start: 0.9172 (mt0) cc_final: 0.8957 (mt0) REVERT: G 59 LYS cc_start: 0.8429 (tttt) cc_final: 0.8194 (tttm) REVERT: G 100 PHE cc_start: 0.8254 (m-80) cc_final: 0.7840 (m-80) REVERT: H 26 ILE cc_start: 0.9300 (tp) cc_final: 0.9070 (tp) REVERT: H 59 LYS cc_start: 0.8829 (tttt) cc_final: 0.8546 (tttp) REVERT: H 79 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8603 (mmtm) REVERT: H 98 TYR cc_start: 0.8434 (m-10) cc_final: 0.8169 (m-10) REVERT: K 284 ASP cc_start: 0.8369 (t70) cc_final: 0.8100 (t0) REVERT: K 296 MET cc_start: 0.8463 (ppp) cc_final: 0.8089 (ppp) REVERT: K 354 MET cc_start: 0.8710 (pmm) cc_final: 0.8320 (pmm) REVERT: K 452 MET cc_start: 0.7928 (ttp) cc_final: 0.7394 (ttm) REVERT: K 556 MET cc_start: 0.9437 (mtm) cc_final: 0.8582 (ptm) REVERT: K 631 MET cc_start: 0.9234 (ptm) cc_final: 0.8820 (ptp) REVERT: K 758 MET cc_start: 0.5691 (tpt) cc_final: 0.5036 (tpp) outliers start: 13 outliers final: 3 residues processed: 288 average time/residue: 0.3469 time to fit residues: 140.3482 Evaluate side-chains 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain H residue 17 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN C 69 HIS D 69 HIS D 115 GLN E 39 HIS E 68 GLN E 113 HIS F 85 GLN F 93 GLN H 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 HIS K 336 HIS ** K 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 639 GLN K 644 HIS K 710 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.088748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057120 restraints weight = 56054.428| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.98 r_work: 0.2828 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17181 Z= 0.334 Angle : 0.705 10.571 24477 Z= 0.392 Chirality : 0.043 0.200 2776 Planarity : 0.005 0.053 2050 Dihedral : 29.550 151.905 4685 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.77 % Allowed : 12.36 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1244 helix: 1.90 (0.18), residues: 803 sheet: -1.38 (0.57), residues: 68 loop : -0.97 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 748 HIS 0.012 0.002 HIS H 18 PHE 0.038 0.002 PHE F 41 TYR 0.017 0.002 TYR K 513 ARG 0.006 0.001 ARG K 431 Details of bonding type rmsd hydrogen bonds : bond 0.06855 ( 735) hydrogen bonds : angle 4.03921 ( 2045) covalent geometry : bond 0.00748 (17181) covalent geometry : angle 0.70507 (24477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9134 (mttp) cc_final: 0.8774 (mttp) REVERT: A 44 LYS cc_start: 0.9257 (ttmm) cc_final: 0.9005 (mtpt) REVERT: A 70 GLU cc_start: 0.8878 (tp30) cc_final: 0.8503 (tp30) REVERT: A 81 ASP cc_start: 0.9036 (m-30) cc_final: 0.8660 (t0) REVERT: A 101 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8744 (mm-30) REVERT: B 73 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8288 (tp30) REVERT: B 81 ASP cc_start: 0.9171 (m-30) cc_final: 0.8961 (m-30) REVERT: B 99 ASP cc_start: 0.8834 (t0) cc_final: 0.8455 (t0) REVERT: B 101 GLU cc_start: 0.8346 (pm20) cc_final: 0.7926 (pm20) REVERT: C 82 MET cc_start: 0.9401 (mmm) cc_final: 0.8976 (tpp) REVERT: C 88 ASP cc_start: 0.9022 (t0) cc_final: 0.8769 (t0) REVERT: C 91 GLU cc_start: 0.8881 (tt0) cc_final: 0.8514 (tp30) REVERT: C 96 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 55 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8191 (mm-30) REVERT: D 88 ASP cc_start: 0.9071 (t0) cc_final: 0.8522 (t0) REVERT: D 91 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 113 GLU cc_start: 0.8871 (mp0) cc_final: 0.8071 (mp0) REVERT: E 50 GLU cc_start: 0.8582 (tt0) cc_final: 0.7977 (tt0) REVERT: E 115 LYS cc_start: 0.9438 (mttm) cc_final: 0.9237 (mmtt) REVERT: E 134 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7879 (mmm160) REVERT: F 53 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8799 (ttpp) REVERT: G 59 LYS cc_start: 0.8989 (tttt) cc_final: 0.8694 (tttm) REVERT: G 100 PHE cc_start: 0.8872 (m-80) cc_final: 0.8589 (m-80) REVERT: H 27 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8792 (mm-40) REVERT: H 79 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8791 (mmtp) REVERT: K 284 ASP cc_start: 0.8665 (t70) cc_final: 0.8356 (t70) REVERT: K 296 MET cc_start: 0.8741 (ppp) cc_final: 0.8418 (ppp) REVERT: K 354 MET cc_start: 0.9036 (pmm) cc_final: 0.8575 (pmm) REVERT: K 452 MET cc_start: 0.8211 (ttp) cc_final: 0.7641 (ttt) REVERT: K 454 ASP cc_start: 0.9382 (p0) cc_final: 0.9027 (t0) REVERT: K 502 LEU cc_start: 0.8523 (tp) cc_final: 0.8147 (tp) REVERT: K 556 MET cc_start: 0.9374 (mtm) cc_final: 0.8475 (ptp) REVERT: K 758 MET cc_start: 0.5327 (tpt) cc_final: 0.4760 (tpp) outliers start: 30 outliers final: 22 residues processed: 223 average time/residue: 0.3418 time to fit residues: 110.9269 Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 343 CYS Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 68 GLN F 39 HIS F 68 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN K 336 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.088477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.057036 restraints weight = 55604.802| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.87 r_work: 0.2840 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17181 Z= 0.210 Angle : 0.566 7.366 24477 Z= 0.322 Chirality : 0.036 0.148 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.349 155.680 4678 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.66 % Allowed : 14.76 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1244 helix: 2.32 (0.18), residues: 804 sheet: -1.52 (0.52), residues: 78 loop : -0.84 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.006 0.001 HIS K 336 PHE 0.019 0.001 PHE E 41 TYR 0.013 0.001 TYR B 66 ARG 0.005 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 735) hydrogen bonds : angle 3.57683 ( 2045) covalent geometry : bond 0.00472 (17181) covalent geometry : angle 0.56589 (24477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9132 (mttp) cc_final: 0.8905 (mttp) REVERT: A 28 MET cc_start: 0.9310 (tmm) cc_final: 0.8901 (tmm) REVERT: A 70 GLU cc_start: 0.8909 (tp30) cc_final: 0.8456 (tp30) REVERT: A 81 ASP cc_start: 0.8993 (m-30) cc_final: 0.8670 (t0) REVERT: A 99 ASP cc_start: 0.8791 (t0) cc_final: 0.8472 (t0) REVERT: B 41 ARG cc_start: 0.9596 (ttp-170) cc_final: 0.9244 (ttp80) REVERT: B 48 TYR cc_start: 0.9552 (m-80) cc_final: 0.9312 (m-80) REVERT: B 73 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8660 (tp30) REVERT: B 83 LYS cc_start: 0.9526 (mmtm) cc_final: 0.9315 (mmmt) REVERT: B 99 ASP cc_start: 0.8780 (t0) cc_final: 0.8343 (t0) REVERT: B 101 GLU cc_start: 0.8222 (pm20) cc_final: 0.7855 (pm20) REVERT: C 88 ASP cc_start: 0.8983 (t0) cc_final: 0.8725 (t0) REVERT: C 91 GLU cc_start: 0.8816 (tt0) cc_final: 0.8560 (tp30) REVERT: C 96 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8358 (mm-30) REVERT: C 113 GLU cc_start: 0.8831 (mp0) cc_final: 0.8027 (mp0) REVERT: D 57 TYR cc_start: 0.9407 (m-80) cc_final: 0.9088 (m-80) REVERT: D 88 ASP cc_start: 0.9066 (t0) cc_final: 0.8514 (t0) REVERT: D 91 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8510 (tm-30) REVERT: D 113 GLU cc_start: 0.8812 (mp0) cc_final: 0.7971 (mp0) REVERT: E 50 GLU cc_start: 0.8584 (tt0) cc_final: 0.7906 (tt0) REVERT: E 115 LYS cc_start: 0.9373 (mttm) cc_final: 0.9123 (mmtm) REVERT: F 50 GLU cc_start: 0.9189 (tt0) cc_final: 0.8963 (tt0) REVERT: G 53 GLU cc_start: 0.8932 (tp30) cc_final: 0.8649 (tp30) REVERT: G 59 LYS cc_start: 0.8931 (tttt) cc_final: 0.8657 (tttm) REVERT: G 100 PHE cc_start: 0.8885 (m-80) cc_final: 0.8541 (m-80) REVERT: H 27 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8825 (mm-40) REVERT: H 79 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8777 (mmtp) REVERT: K 296 MET cc_start: 0.8932 (ppp) cc_final: 0.8592 (ppp) REVERT: K 344 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8714 (mmtp) REVERT: K 354 MET cc_start: 0.8971 (pmm) cc_final: 0.8528 (pmm) REVERT: K 373 TRP cc_start: 0.9222 (t60) cc_final: 0.8918 (t60) REVERT: K 452 MET cc_start: 0.8116 (ttp) cc_final: 0.7476 (ttt) REVERT: K 556 MET cc_start: 0.9332 (mtm) cc_final: 0.8458 (ptp) REVERT: K 758 MET cc_start: 0.5241 (tpt) cc_final: 0.4799 (mmm) outliers start: 18 outliers final: 13 residues processed: 199 average time/residue: 0.3121 time to fit residues: 92.9384 Evaluate side-chains 192 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 142 optimal weight: 0.0570 chunk 151 optimal weight: 5.9990 chunk 64 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.0050 chunk 100 optimal weight: 6.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 39 HIS F 113 HIS G 93 GLN H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.090324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059561 restraints weight = 54531.441| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.86 r_work: 0.2905 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17181 Z= 0.137 Angle : 0.527 8.078 24477 Z= 0.302 Chirality : 0.033 0.140 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.064 156.668 4678 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.11 % Allowed : 16.33 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1244 helix: 2.54 (0.18), residues: 804 sheet: -1.13 (0.56), residues: 68 loop : -0.67 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.025 0.001 HIS K 499 PHE 0.009 0.001 PHE F 67 TYR 0.012 0.001 TYR K 513 ARG 0.012 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 735) hydrogen bonds : angle 3.28364 ( 2045) covalent geometry : bond 0.00294 (17181) covalent geometry : angle 0.52698 (24477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8799 (tp30) cc_final: 0.8432 (tp30) REVERT: A 81 ASP cc_start: 0.9013 (m-30) cc_final: 0.8526 (t0) REVERT: A 83 LYS cc_start: 0.9385 (mptt) cc_final: 0.9152 (mppt) REVERT: A 99 ASP cc_start: 0.8942 (t0) cc_final: 0.8308 (t0) REVERT: B 28 MET cc_start: 0.8663 (ppp) cc_final: 0.8416 (ppp) REVERT: B 41 ARG cc_start: 0.9552 (ttp-170) cc_final: 0.9173 (ttp80) REVERT: B 73 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8304 (tp30) REVERT: B 99 ASP cc_start: 0.8781 (t0) cc_final: 0.8194 (t0) REVERT: B 101 GLU cc_start: 0.8249 (pm20) cc_final: 0.7870 (pm20) REVERT: C 88 ASP cc_start: 0.8905 (t0) cc_final: 0.8575 (t0) REVERT: C 96 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 113 GLU cc_start: 0.8865 (mp0) cc_final: 0.8030 (mp0) REVERT: D 57 TYR cc_start: 0.9358 (m-80) cc_final: 0.9072 (m-80) REVERT: D 88 ASP cc_start: 0.9051 (t0) cc_final: 0.8488 (t0) REVERT: D 91 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 113 GLU cc_start: 0.8723 (mp0) cc_final: 0.8037 (mp0) REVERT: D 125 GLU cc_start: 0.8356 (tp30) cc_final: 0.8118 (tp30) REVERT: E 50 GLU cc_start: 0.8570 (tt0) cc_final: 0.7958 (tt0) REVERT: E 115 LYS cc_start: 0.9358 (mttm) cc_final: 0.9083 (mptt) REVERT: E 133 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8404 (pt0) REVERT: F 125 GLN cc_start: 0.9552 (mt0) cc_final: 0.9350 (mt0) REVERT: G 59 LYS cc_start: 0.8837 (tttt) cc_final: 0.8618 (tttm) REVERT: G 100 PHE cc_start: 0.8863 (m-80) cc_final: 0.8583 (m-80) REVERT: H 27 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8697 (mm-40) REVERT: H 79 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8861 (mmtm) REVERT: K 296 MET cc_start: 0.9066 (ppp) cc_final: 0.8813 (ppp) REVERT: K 354 MET cc_start: 0.8695 (pmm) cc_final: 0.8253 (pmm) REVERT: K 373 TRP cc_start: 0.9218 (t60) cc_final: 0.8950 (t60) REVERT: K 452 MET cc_start: 0.8047 (ttp) cc_final: 0.7309 (ttt) REVERT: K 499 HIS cc_start: 0.5859 (p-80) cc_final: 0.5441 (p-80) REVERT: K 502 LEU cc_start: 0.8253 (tp) cc_final: 0.7944 (tp) REVERT: K 622 TRP cc_start: 0.9207 (m100) cc_final: 0.7574 (m100) REVERT: K 626 MET cc_start: 0.8806 (tpp) cc_final: 0.8547 (mmt) REVERT: K 758 MET cc_start: 0.5224 (tpt) cc_final: 0.4779 (mmm) outliers start: 12 outliers final: 10 residues processed: 211 average time/residue: 0.3868 time to fit residues: 120.5390 Evaluate side-chains 196 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 43 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS G 93 GLN H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054329 restraints weight = 56719.545| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.88 r_work: 0.2779 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17181 Z= 0.289 Angle : 0.628 8.800 24477 Z= 0.352 Chirality : 0.039 0.137 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.655 160.495 4678 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.21 % Allowed : 17.80 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1244 helix: 2.43 (0.18), residues: 813 sheet: -1.45 (0.53), residues: 78 loop : -0.73 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 373 HIS 0.024 0.001 HIS K 499 PHE 0.014 0.002 PHE F 78 TYR 0.014 0.002 TYR C 57 ARG 0.005 0.001 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.06023 ( 735) hydrogen bonds : angle 3.80980 ( 2045) covalent geometry : bond 0.00648 (17181) covalent geometry : angle 0.62834 (24477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9128 (mttp) cc_final: 0.8653 (mttp) REVERT: A 28 MET cc_start: 0.9386 (tmm) cc_final: 0.9008 (tmm) REVERT: A 70 GLU cc_start: 0.8937 (tp30) cc_final: 0.8482 (tp30) REVERT: A 73 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 81 ASP cc_start: 0.9010 (m-30) cc_final: 0.8711 (t0) REVERT: A 99 ASP cc_start: 0.8980 (t0) cc_final: 0.8265 (t0) REVERT: B 41 ARG cc_start: 0.9612 (ttp-170) cc_final: 0.9238 (ttp80) REVERT: B 47 ARG cc_start: 0.9219 (ptm160) cc_final: 0.8983 (mtm110) REVERT: B 73 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8351 (tp30) REVERT: B 99 ASP cc_start: 0.8866 (t0) cc_final: 0.8370 (t0) REVERT: B 101 GLU cc_start: 0.8364 (pm20) cc_final: 0.7940 (pm20) REVERT: C 88 ASP cc_start: 0.8987 (t0) cc_final: 0.8749 (t0) REVERT: C 96 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 113 GLU cc_start: 0.8896 (mp0) cc_final: 0.8073 (mp0) REVERT: C 129 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8834 (m-70) REVERT: D 57 TYR cc_start: 0.9487 (m-80) cc_final: 0.9114 (m-80) REVERT: D 88 ASP cc_start: 0.9088 (t0) cc_final: 0.8543 (t0) REVERT: D 91 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8492 (tm-30) REVERT: D 97 SER cc_start: 0.9386 (m) cc_final: 0.9057 (p) REVERT: D 125 GLU cc_start: 0.8638 (tp30) cc_final: 0.8246 (tp30) REVERT: E 54 TYR cc_start: 0.9030 (m-80) cc_final: 0.8614 (m-80) REVERT: E 115 LYS cc_start: 0.9455 (mttm) cc_final: 0.9211 (mmtt) REVERT: E 120 MET cc_start: 0.9022 (mtp) cc_final: 0.8582 (mtp) REVERT: F 50 GLU cc_start: 0.9181 (tt0) cc_final: 0.8502 (tt0) REVERT: G 53 GLU cc_start: 0.8871 (tp30) cc_final: 0.8437 (tp30) REVERT: G 59 LYS cc_start: 0.8967 (tttt) cc_final: 0.8710 (tttm) REVERT: G 100 PHE cc_start: 0.9030 (m-80) cc_final: 0.8773 (m-80) REVERT: H 79 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8894 (mmtm) REVERT: K 354 MET cc_start: 0.8791 (pmm) cc_final: 0.8128 (pmm) REVERT: K 452 MET cc_start: 0.8168 (ttp) cc_final: 0.7851 (ttm) REVERT: K 502 LEU cc_start: 0.8360 (tp) cc_final: 0.8073 (tp) REVERT: K 758 MET cc_start: 0.5276 (tpt) cc_final: 0.4824 (mmm) outliers start: 24 outliers final: 17 residues processed: 200 average time/residue: 0.3180 time to fit residues: 95.2131 Evaluate side-chains 193 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 39 HIS G 93 GLN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 ASN ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054691 restraints weight = 56458.392| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.86 r_work: 0.2797 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17181 Z= 0.236 Angle : 0.578 9.974 24477 Z= 0.328 Chirality : 0.036 0.142 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.534 162.984 4678 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 17.90 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.24), residues: 1244 helix: 2.57 (0.18), residues: 813 sheet: -1.38 (0.53), residues: 78 loop : -0.61 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.007 0.001 HIS C 129 PHE 0.012 0.001 PHE G 100 TYR 0.015 0.001 TYR B 48 ARG 0.004 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 735) hydrogen bonds : angle 3.54586 ( 2045) covalent geometry : bond 0.00526 (17181) covalent geometry : angle 0.57826 (24477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9146 (mttp) cc_final: 0.8632 (mttp) REVERT: A 70 GLU cc_start: 0.8896 (tp30) cc_final: 0.8448 (tp30) REVERT: A 73 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 81 ASP cc_start: 0.8997 (m-30) cc_final: 0.8764 (t0) REVERT: A 99 ASP cc_start: 0.8949 (t0) cc_final: 0.8268 (t0) REVERT: A 113 HIS cc_start: 0.9025 (m-70) cc_final: 0.8773 (m-70) REVERT: B 28 MET cc_start: 0.8674 (ppp) cc_final: 0.8460 (ppp) REVERT: B 41 ARG cc_start: 0.9586 (ttp-170) cc_final: 0.9191 (ttp80) REVERT: B 47 ARG cc_start: 0.9293 (ptm160) cc_final: 0.9027 (mtm110) REVERT: B 73 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8443 (tp30) REVERT: B 99 ASP cc_start: 0.8849 (t0) cc_final: 0.8222 (t0) REVERT: B 101 GLU cc_start: 0.8427 (pm20) cc_final: 0.8067 (pm20) REVERT: C 88 ASP cc_start: 0.8972 (t0) cc_final: 0.8728 (t0) REVERT: C 91 GLU cc_start: 0.9254 (tp30) cc_final: 0.8905 (tp30) REVERT: C 96 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8362 (mm-30) REVERT: C 113 GLU cc_start: 0.8863 (mp0) cc_final: 0.8026 (mp0) REVERT: C 129 HIS cc_start: 0.9187 (OUTLIER) cc_final: 0.8676 (m-70) REVERT: D 55 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8868 (mm-30) REVERT: D 57 TYR cc_start: 0.9451 (m-80) cc_final: 0.9152 (m-80) REVERT: D 88 ASP cc_start: 0.9082 (t0) cc_final: 0.8650 (t0) REVERT: D 91 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 97 SER cc_start: 0.9389 (m) cc_final: 0.9064 (p) REVERT: D 113 GLU cc_start: 0.8807 (mp0) cc_final: 0.8179 (mp0) REVERT: D 125 GLU cc_start: 0.8589 (tp30) cc_final: 0.8194 (tp30) REVERT: E 50 GLU cc_start: 0.8666 (tt0) cc_final: 0.7973 (tt0) REVERT: E 54 TYR cc_start: 0.9055 (m-80) cc_final: 0.8697 (m-80) REVERT: E 115 LYS cc_start: 0.9402 (mttm) cc_final: 0.9168 (mmtt) REVERT: F 50 GLU cc_start: 0.9205 (tt0) cc_final: 0.8988 (tt0) REVERT: G 59 LYS cc_start: 0.8930 (tttt) cc_final: 0.8689 (tttm) REVERT: H 79 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8933 (mmtm) REVERT: H 98 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: K 296 MET cc_start: 0.8924 (ppp) cc_final: 0.8724 (ppp) REVERT: K 354 MET cc_start: 0.8665 (pmm) cc_final: 0.8049 (pmm) REVERT: K 452 MET cc_start: 0.8102 (ttp) cc_final: 0.7837 (ttt) REVERT: K 502 LEU cc_start: 0.8004 (tp) cc_final: 0.7763 (tp) REVERT: K 758 MET cc_start: 0.5495 (tpt) cc_final: 0.5088 (mmm) outliers start: 23 outliers final: 18 residues processed: 195 average time/residue: 0.3525 time to fit residues: 102.3334 Evaluate side-chains 198 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 39 HIS H 18 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 608 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.085782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055104 restraints weight = 55871.496| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.88 r_work: 0.2802 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17181 Z= 0.212 Angle : 0.569 9.684 24477 Z= 0.322 Chirality : 0.035 0.132 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.546 168.656 4678 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.94 % Allowed : 18.45 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.24), residues: 1244 helix: 2.67 (0.18), residues: 810 sheet: -1.38 (0.53), residues: 78 loop : -0.55 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.006 0.001 HIS C 129 PHE 0.010 0.001 PHE G 100 TYR 0.012 0.001 TYR B 48 ARG 0.004 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 735) hydrogen bonds : angle 3.47841 ( 2045) covalent geometry : bond 0.00472 (17181) covalent geometry : angle 0.56912 (24477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9115 (mttp) cc_final: 0.8610 (mttp) REVERT: A 70 GLU cc_start: 0.8927 (tp30) cc_final: 0.8458 (tp30) REVERT: A 73 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 81 ASP cc_start: 0.9013 (m-30) cc_final: 0.8786 (t0) REVERT: A 99 ASP cc_start: 0.8971 (t0) cc_final: 0.8257 (t0) REVERT: A 113 HIS cc_start: 0.9071 (m-70) cc_final: 0.8791 (m-70) REVERT: B 41 ARG cc_start: 0.9573 (ttp-170) cc_final: 0.9136 (ttp80) REVERT: B 47 ARG cc_start: 0.9274 (ptm160) cc_final: 0.9036 (mtm110) REVERT: B 73 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8666 (tp30) REVERT: B 99 ASP cc_start: 0.8801 (t0) cc_final: 0.8143 (t0) REVERT: B 101 GLU cc_start: 0.8409 (pm20) cc_final: 0.7973 (pm20) REVERT: C 88 ASP cc_start: 0.8977 (t0) cc_final: 0.8730 (t0) REVERT: C 91 GLU cc_start: 0.9247 (tp30) cc_final: 0.8903 (tp30) REVERT: C 96 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 113 GLU cc_start: 0.8948 (mp0) cc_final: 0.8075 (mp0) REVERT: D 55 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8853 (mm-30) REVERT: D 57 TYR cc_start: 0.9462 (m-80) cc_final: 0.9050 (m-80) REVERT: D 88 ASP cc_start: 0.9091 (t0) cc_final: 0.8648 (t0) REVERT: D 91 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 97 SER cc_start: 0.9389 (m) cc_final: 0.9055 (p) REVERT: D 113 GLU cc_start: 0.8781 (mp0) cc_final: 0.8078 (mp0) REVERT: D 125 GLU cc_start: 0.8608 (tp30) cc_final: 0.8196 (tp30) REVERT: E 50 GLU cc_start: 0.8669 (tt0) cc_final: 0.7970 (tt0) REVERT: E 54 TYR cc_start: 0.9008 (m-80) cc_final: 0.8630 (m-80) REVERT: E 115 LYS cc_start: 0.9444 (mttm) cc_final: 0.9173 (mptt) REVERT: F 50 GLU cc_start: 0.9203 (tt0) cc_final: 0.8969 (tt0) REVERT: F 94 GLU cc_start: 0.9200 (tp30) cc_final: 0.8931 (tt0) REVERT: G 53 GLU cc_start: 0.8923 (tp30) cc_final: 0.8684 (tp30) REVERT: G 59 LYS cc_start: 0.8916 (tttt) cc_final: 0.8696 (tttm) REVERT: H 79 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8948 (mmtm) REVERT: H 98 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: K 354 MET cc_start: 0.8721 (pmm) cc_final: 0.8069 (pmm) REVERT: K 452 MET cc_start: 0.7964 (ttp) cc_final: 0.7586 (ttt) REVERT: K 758 MET cc_start: 0.5470 (tpt) cc_final: 0.5060 (mmm) outliers start: 21 outliers final: 16 residues processed: 195 average time/residue: 0.3139 time to fit residues: 89.6943 Evaluate side-chains 194 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.085823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055387 restraints weight = 56092.441| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.85 r_work: 0.2819 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17181 Z= 0.188 Angle : 0.562 12.205 24477 Z= 0.317 Chirality : 0.034 0.157 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.501 172.697 4678 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.48 % Allowed : 18.54 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1244 helix: 2.74 (0.18), residues: 810 sheet: -1.37 (0.52), residues: 78 loop : -0.50 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.005 0.001 HIS C 129 PHE 0.009 0.001 PHE F 67 TYR 0.013 0.001 TYR B 48 ARG 0.007 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 735) hydrogen bonds : angle 3.37011 ( 2045) covalent geometry : bond 0.00417 (17181) covalent geometry : angle 0.56230 (24477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9128 (mttp) cc_final: 0.8615 (mttp) REVERT: A 70 GLU cc_start: 0.8900 (tp30) cc_final: 0.8423 (tp30) REVERT: A 73 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 81 ASP cc_start: 0.8998 (m-30) cc_final: 0.8787 (t0) REVERT: A 99 ASP cc_start: 0.8933 (t0) cc_final: 0.8197 (t0) REVERT: B 41 ARG cc_start: 0.9581 (ttp-170) cc_final: 0.9116 (ttp80) REVERT: B 47 ARG cc_start: 0.9275 (ptm160) cc_final: 0.8976 (ptm160) REVERT: B 73 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8332 (tp30) REVERT: B 99 ASP cc_start: 0.8885 (t0) cc_final: 0.8267 (t0) REVERT: B 101 GLU cc_start: 0.8376 (pm20) cc_final: 0.8037 (pm20) REVERT: C 88 ASP cc_start: 0.8955 (t0) cc_final: 0.8712 (t0) REVERT: C 91 GLU cc_start: 0.9245 (tp30) cc_final: 0.8898 (tp30) REVERT: C 96 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8437 (mm-30) REVERT: C 113 GLU cc_start: 0.8919 (mp0) cc_final: 0.8048 (mp0) REVERT: C 129 HIS cc_start: 0.9122 (OUTLIER) cc_final: 0.8820 (m-70) REVERT: D 55 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8943 (mm-30) REVERT: D 57 TYR cc_start: 0.9440 (m-80) cc_final: 0.9045 (m-80) REVERT: D 88 ASP cc_start: 0.9091 (t0) cc_final: 0.8652 (t0) REVERT: D 91 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8548 (tm-30) REVERT: D 97 SER cc_start: 0.9387 (m) cc_final: 0.9048 (p) REVERT: D 113 GLU cc_start: 0.8791 (mp0) cc_final: 0.8081 (mp0) REVERT: D 125 GLU cc_start: 0.8544 (tp30) cc_final: 0.8156 (tp30) REVERT: E 50 GLU cc_start: 0.8664 (tt0) cc_final: 0.7971 (tt0) REVERT: E 54 TYR cc_start: 0.9035 (m-80) cc_final: 0.8676 (m-80) REVERT: E 115 LYS cc_start: 0.9467 (mttm) cc_final: 0.9211 (mptt) REVERT: F 50 GLU cc_start: 0.9215 (tt0) cc_final: 0.8959 (tt0) REVERT: G 53 GLU cc_start: 0.8891 (tp30) cc_final: 0.8624 (tp30) REVERT: G 59 LYS cc_start: 0.8930 (tttt) cc_final: 0.8721 (tttm) REVERT: H 79 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8962 (mmtm) REVERT: H 98 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: K 354 MET cc_start: 0.8710 (pmm) cc_final: 0.8045 (pmm) REVERT: K 373 TRP cc_start: 0.9150 (t60) cc_final: 0.8846 (t60) REVERT: K 452 MET cc_start: 0.7961 (ttp) cc_final: 0.7533 (ttt) REVERT: K 758 MET cc_start: 0.5461 (tpt) cc_final: 0.5047 (mmm) outliers start: 16 outliers final: 14 residues processed: 191 average time/residue: 0.3123 time to fit residues: 88.2902 Evaluate side-chains 194 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.084708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054018 restraints weight = 56615.277| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.89 r_work: 0.2775 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17181 Z= 0.245 Angle : 0.602 10.497 24477 Z= 0.337 Chirality : 0.036 0.151 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.734 175.299 4678 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.75 % Allowed : 19.37 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1244 helix: 2.67 (0.18), residues: 813 sheet: -1.47 (0.52), residues: 78 loop : -0.49 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.005 0.001 HIS C 129 PHE 0.012 0.001 PHE G 100 TYR 0.016 0.002 TYR B 48 ARG 0.006 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.05244 ( 735) hydrogen bonds : angle 3.54070 ( 2045) covalent geometry : bond 0.00549 (17181) covalent geometry : angle 0.60179 (24477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9141 (mttp) cc_final: 0.8689 (mttp) REVERT: A 70 GLU cc_start: 0.8907 (tp30) cc_final: 0.8451 (tp30) REVERT: A 73 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8709 (tm-30) REVERT: A 81 ASP cc_start: 0.9015 (m-30) cc_final: 0.8789 (t0) REVERT: A 99 ASP cc_start: 0.8964 (t0) cc_final: 0.8245 (t0) REVERT: B 41 ARG cc_start: 0.9549 (ttp-170) cc_final: 0.9181 (ttp80) REVERT: B 47 ARG cc_start: 0.9287 (ptm160) cc_final: 0.8993 (mtm110) REVERT: B 70 GLU cc_start: 0.8973 (tp30) cc_final: 0.8727 (tp30) REVERT: B 73 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8470 (tp30) REVERT: B 99 ASP cc_start: 0.8798 (t0) cc_final: 0.7882 (t0) REVERT: B 101 GLU cc_start: 0.8334 (pm20) cc_final: 0.8126 (pm20) REVERT: C 88 ASP cc_start: 0.8982 (t0) cc_final: 0.8735 (t0) REVERT: C 91 GLU cc_start: 0.9272 (tp30) cc_final: 0.8972 (tp30) REVERT: C 96 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8436 (mm-30) REVERT: C 113 GLU cc_start: 0.8888 (mp0) cc_final: 0.8021 (mp0) REVERT: D 55 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8895 (mm-30) REVERT: D 57 TYR cc_start: 0.9468 (m-80) cc_final: 0.9030 (m-80) REVERT: D 88 ASP cc_start: 0.9096 (t0) cc_final: 0.8639 (t0) REVERT: D 91 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 97 SER cc_start: 0.9395 (m) cc_final: 0.9053 (p) REVERT: D 113 GLU cc_start: 0.8833 (mp0) cc_final: 0.8421 (mp0) REVERT: D 125 GLU cc_start: 0.8642 (tp30) cc_final: 0.8209 (tp30) REVERT: E 50 GLU cc_start: 0.8692 (tt0) cc_final: 0.8010 (tt0) REVERT: E 54 TYR cc_start: 0.9079 (m-80) cc_final: 0.8736 (m-80) REVERT: E 115 LYS cc_start: 0.9479 (mttm) cc_final: 0.9241 (mmtt) REVERT: F 50 GLU cc_start: 0.9194 (tt0) cc_final: 0.8960 (tt0) REVERT: G 53 GLU cc_start: 0.8983 (tp30) cc_final: 0.8708 (tp30) REVERT: G 59 LYS cc_start: 0.8949 (tttt) cc_final: 0.8733 (tttm) REVERT: H 98 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8408 (m-10) REVERT: K 296 MET cc_start: 0.8753 (ppp) cc_final: 0.8486 (ppp) REVERT: K 354 MET cc_start: 0.8787 (pmm) cc_final: 0.8161 (pmm) REVERT: K 373 TRP cc_start: 0.9150 (t60) cc_final: 0.8821 (t60) REVERT: K 452 MET cc_start: 0.7949 (ttp) cc_final: 0.7534 (ttt) REVERT: K 758 MET cc_start: 0.5581 (tpt) cc_final: 0.5133 (mmm) outliers start: 19 outliers final: 17 residues processed: 188 average time/residue: 0.2905 time to fit residues: 81.0162 Evaluate side-chains 192 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 502 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 124 optimal weight: 30.0000 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.085831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.055640 restraints weight = 56783.238| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.88 r_work: 0.2832 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17181 Z= 0.160 Angle : 0.559 10.014 24477 Z= 0.315 Chirality : 0.034 0.174 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.545 177.377 4678 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.20 % Allowed : 20.20 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.24), residues: 1244 helix: 2.74 (0.18), residues: 810 sheet: -1.32 (0.52), residues: 78 loop : -0.41 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.004 0.001 HIS C 129 PHE 0.009 0.001 PHE F 67 TYR 0.013 0.001 TYR B 48 ARG 0.007 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 735) hydrogen bonds : angle 3.29980 ( 2045) covalent geometry : bond 0.00354 (17181) covalent geometry : angle 0.55858 (24477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9120 (mttp) cc_final: 0.8663 (mttp) REVERT: A 70 GLU cc_start: 0.8892 (tp30) cc_final: 0.8421 (tp30) REVERT: A 73 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 99 ASP cc_start: 0.8952 (t0) cc_final: 0.8242 (t0) REVERT: B 41 ARG cc_start: 0.9552 (ttp-170) cc_final: 0.9170 (ttp80) REVERT: B 47 ARG cc_start: 0.9237 (ptm160) cc_final: 0.8957 (ptm160) REVERT: B 73 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8320 (tp30) REVERT: B 99 ASP cc_start: 0.8887 (t0) cc_final: 0.7971 (t0) REVERT: B 101 GLU cc_start: 0.8336 (pm20) cc_final: 0.8054 (pm20) REVERT: C 88 ASP cc_start: 0.8949 (t0) cc_final: 0.8705 (t0) REVERT: C 113 GLU cc_start: 0.8905 (mp0) cc_final: 0.8072 (mp0) REVERT: C 129 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8899 (m-70) REVERT: D 55 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8979 (mm-30) REVERT: D 57 TYR cc_start: 0.9433 (m-80) cc_final: 0.9092 (m-80) REVERT: D 88 ASP cc_start: 0.9076 (t0) cc_final: 0.8518 (t0) REVERT: D 91 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8526 (tm-30) REVERT: D 97 SER cc_start: 0.9388 (m) cc_final: 0.9043 (p) REVERT: D 113 GLU cc_start: 0.8816 (mp0) cc_final: 0.8097 (mp0) REVERT: D 125 GLU cc_start: 0.8507 (tp30) cc_final: 0.8117 (tp30) REVERT: E 50 GLU cc_start: 0.8699 (tt0) cc_final: 0.7973 (tt0) REVERT: E 54 TYR cc_start: 0.9018 (m-80) cc_final: 0.8657 (m-80) REVERT: E 115 LYS cc_start: 0.9446 (mttm) cc_final: 0.9186 (mptt) REVERT: F 50 GLU cc_start: 0.9219 (tt0) cc_final: 0.8953 (tt0) REVERT: G 53 GLU cc_start: 0.8874 (tp30) cc_final: 0.8588 (tp30) REVERT: G 59 LYS cc_start: 0.8917 (tttt) cc_final: 0.8716 (tttm) REVERT: K 296 MET cc_start: 0.8783 (ppp) cc_final: 0.8511 (ppp) REVERT: K 354 MET cc_start: 0.8712 (pmm) cc_final: 0.8087 (pmm) REVERT: K 373 TRP cc_start: 0.9209 (t60) cc_final: 0.8915 (t60) REVERT: K 452 MET cc_start: 0.7897 (ttp) cc_final: 0.7412 (ttt) outliers start: 13 outliers final: 12 residues processed: 189 average time/residue: 0.2873 time to fit residues: 81.0048 Evaluate side-chains 193 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 502 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.087341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057285 restraints weight = 55654.833| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.87 r_work: 0.2869 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17181 Z= 0.143 Angle : 0.556 11.604 24477 Z= 0.311 Chirality : 0.033 0.170 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.381 177.667 4678 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.01 % Allowed : 20.85 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.24), residues: 1244 helix: 2.75 (0.18), residues: 809 sheet: -1.26 (0.51), residues: 78 loop : -0.39 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.004 0.001 HIS C 129 PHE 0.008 0.001 PHE F 67 TYR 0.012 0.001 TYR B 48 ARG 0.006 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 735) hydrogen bonds : angle 3.20759 ( 2045) covalent geometry : bond 0.00312 (17181) covalent geometry : angle 0.55566 (24477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10311.07 seconds wall clock time: 183 minutes 51.38 seconds (11031.38 seconds total)