Starting phenix.real_space_refine on Sun Aug 24 01:44:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcc_37099/08_2025/8kcc_37099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcc_37099/08_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_37099/08_2025/8kcc_37099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2025/8kcc_37099.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2025/8kcc_37099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2025/8kcc_37099.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'ARG: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: 3.43, per 1000 atoms: 0.21 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: 1.08 Conformation dependent library (CDL) restraints added in 516.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.20 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: 3.40 Time building geometry restraints manager: 1.41 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG H 17 TYR 0.008 0.001 TYR B 66 PHE 0.012 0.001 PHE K 459 TRP 0.004 0.001 TRP K 212 HIS 0.010 0.001 HIS K 670 Details of bonding type rmsd covalent geometry : bond 0.00433 (17181) covalent geometry : angle 0.55008 (24477) hydrogen bonds : bond 0.17466 ( 735) hydrogen bonds : angle 6.49654 ( 2045) *********************** 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 : 0.496 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: 0.1410 time to fit residues: 57.2090 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 : 0.445 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 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 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.086499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055084 restraints weight = 55921.407| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.00 r_work: 0.2779 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.126 17181 Z= 0.428 Angle : 0.779 10.175 24477 Z= 0.434 Chirality : 0.047 0.218 2776 Planarity : 0.006 0.060 2050 Dihedral : 29.758 153.503 4685 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.41 % Allowed : 12.36 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.24), residues: 1244 helix: 1.79 (0.18), residues: 803 sheet: -1.65 (0.53), residues: 78 loop : -1.03 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 42 TYR 0.014 0.002 TYR B 66 PHE 0.030 0.002 PHE F 41 TRP 0.014 0.002 TRP K 748 HIS 0.009 0.002 HIS K 670 Details of bonding type rmsd covalent geometry : bond 0.00956 (17181) covalent geometry : angle 0.77915 (24477) hydrogen bonds : bond 0.07343 ( 735) hydrogen bonds : angle 4.32087 ( 2045) *********************** 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 227 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9122 (mttp) cc_final: 0.8783 (mttp) REVERT: A 44 LYS cc_start: 0.9287 (ttmm) cc_final: 0.8999 (mtpt) REVERT: A 70 GLU cc_start: 0.8910 (tp30) cc_final: 0.8533 (tp30) REVERT: A 73 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8771 (tm-30) REVERT: A 81 ASP cc_start: 0.9054 (m-30) cc_final: 0.8680 (t0) REVERT: B 70 GLU cc_start: 0.9062 (tp30) cc_final: 0.8841 (tp30) REVERT: B 73 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8315 (tp30) REVERT: B 83 LYS cc_start: 0.9533 (mmtm) cc_final: 0.9320 (mmmt) REVERT: B 99 ASP cc_start: 0.8777 (t0) cc_final: 0.8496 (t0) REVERT: C 67 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.8934 (tm-30) REVERT: C 82 MET cc_start: 0.9414 (mmm) cc_final: 0.8997 (tpp) REVERT: C 88 ASP cc_start: 0.9020 (t0) cc_final: 0.8771 (t0) REVERT: C 91 GLU cc_start: 0.8898 (tt0) cc_final: 0.8636 (tp30) REVERT: C 96 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 88 ASP cc_start: 0.9083 (t0) cc_final: 0.8552 (t0) REVERT: D 91 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8630 (tm-30) REVERT: D 113 GLU cc_start: 0.8837 (mp0) cc_final: 0.8056 (mp0) REVERT: F 53 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8796 (ttpp) REVERT: G 53 GLU cc_start: 0.8961 (tp30) cc_final: 0.8572 (tp30) REVERT: G 59 LYS cc_start: 0.8991 (tttt) cc_final: 0.8673 (tttm) REVERT: H 16 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8461 (mmtm) REVERT: H 24 ASP cc_start: 0.8749 (t0) cc_final: 0.8274 (p0) REVERT: H 79 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8810 (mmtm) REVERT: K 296 MET cc_start: 0.8711 (ppp) cc_final: 0.8382 (ppp) REVERT: K 354 MET cc_start: 0.9046 (pmm) cc_final: 0.8564 (pmm) REVERT: K 452 MET cc_start: 0.8354 (ttp) cc_final: 0.7925 (ttt) REVERT: K 454 ASP cc_start: 0.9472 (p0) cc_final: 0.9083 (t0) REVERT: K 502 LEU cc_start: 0.8441 (tp) cc_final: 0.8104 (tp) REVERT: K 758 MET cc_start: 0.5330 (tpt) cc_final: 0.4739 (tpp) outliers start: 37 outliers final: 28 residues processed: 216 average time/residue: 0.1259 time to fit residues: 39.7725 Evaluate side-chains 201 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 126 LEU 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 89 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 E residue 107 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 74 ILE 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 194 CYS Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 528 LEU 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 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 HIS E 39 HIS E 68 GLN F 39 HIS F 68 GLN G 93 GLN H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN K 336 HIS K 351 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058069 restraints weight = 55953.553| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.94 r_work: 0.2861 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3814 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= 0.157 Angle : 0.545 7.572 24477 Z= 0.313 Chirality : 0.035 0.143 2776 Planarity : 0.004 0.050 2050 Dihedral : 29.338 155.289 4678 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.29 % Allowed : 15.41 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.24), residues: 1244 helix: 2.27 (0.18), residues: 805 sheet: -1.21 (0.56), residues: 68 loop : -0.80 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 47 TYR 0.015 0.001 TYR B 48 PHE 0.009 0.001 PHE F 67 TRP 0.012 0.001 TRP K 373 HIS 0.007 0.001 HIS K 336 Details of bonding type rmsd covalent geometry : bond 0.00344 (17181) covalent geometry : angle 0.54473 (24477) hydrogen bonds : bond 0.04563 ( 735) hydrogen bonds : angle 3.49018 ( 2045) *********************** 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 216 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9215 (tmm) REVERT: A 50 GLN cc_start: 0.8645 (mp10) cc_final: 0.8346 (mp10) REVERT: A 70 GLU cc_start: 0.8811 (tp30) cc_final: 0.8436 (tp30) REVERT: A 73 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 81 ASP cc_start: 0.8972 (m-30) cc_final: 0.8712 (t0) REVERT: B 41 ARG cc_start: 0.9576 (ttp-170) cc_final: 0.9183 (ttp80) REVERT: B 47 ARG cc_start: 0.9161 (ptm160) cc_final: 0.8895 (mtm110) REVERT: B 73 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8684 (tp30) REVERT: B 99 ASP cc_start: 0.8742 (t0) cc_final: 0.8181 (t0) REVERT: B 101 GLU cc_start: 0.8203 (pm20) cc_final: 0.7917 (pm20) REVERT: C 88 ASP cc_start: 0.8979 (t0) cc_final: 0.8711 (t0) REVERT: C 91 GLU cc_start: 0.8849 (tt0) cc_final: 0.8566 (tp30) REVERT: C 96 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 113 GLU cc_start: 0.8796 (mp0) cc_final: 0.8026 (mp0) REVERT: D 55 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7271 (mm-30) REVERT: D 57 TYR cc_start: 0.9383 (m-80) cc_final: 0.9014 (m-80) REVERT: D 88 ASP cc_start: 0.9048 (t0) cc_final: 0.8493 (t0) REVERT: D 91 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8473 (tm-30) REVERT: D 113 GLU cc_start: 0.8807 (mp0) cc_final: 0.7954 (mp0) REVERT: E 50 GLU cc_start: 0.8535 (tt0) cc_final: 0.7854 (tt0) REVERT: E 115 LYS cc_start: 0.9356 (mttm) cc_final: 0.9109 (mmtm) REVERT: E 134 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7697 (mmm160) REVERT: F 50 GLU cc_start: 0.9189 (tt0) cc_final: 0.8950 (tt0) REVERT: G 59 LYS cc_start: 0.8868 (tttt) cc_final: 0.8603 (tttm) REVERT: G 100 PHE cc_start: 0.8892 (m-80) cc_final: 0.8556 (m-80) REVERT: H 16 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8520 (mmtm) REVERT: H 24 ASP cc_start: 0.8810 (t0) cc_final: 0.8310 (p0) REVERT: H 79 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8855 (mmtm) REVERT: K 231 LEU cc_start: 0.8775 (mp) cc_final: 0.8574 (tt) REVERT: K 296 MET cc_start: 0.9047 (ppp) cc_final: 0.8758 (ppp) REVERT: K 354 MET cc_start: 0.8955 (pmm) cc_final: 0.8496 (pmm) REVERT: K 373 TRP cc_start: 0.9251 (t60) cc_final: 0.8962 (t60) REVERT: K 452 MET cc_start: 0.8098 (ttp) cc_final: 0.7471 (ttt) REVERT: K 626 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8552 (tpp) REVERT: K 758 MET cc_start: 0.5203 (tpt) cc_final: 0.4763 (mmm) outliers start: 14 outliers final: 7 residues processed: 209 average time/residue: 0.1350 time to fit residues: 41.5676 Evaluate side-chains 195 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET 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 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 626 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS F 113 HIS G 93 GLN H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 541 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.088618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057914 restraints weight = 55581.152| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.85 r_work: 0.2864 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17181 Z= 0.164 Angle : 0.538 8.813 24477 Z= 0.308 Chirality : 0.034 0.139 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.174 157.099 4678 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.66 % Allowed : 16.88 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.24), residues: 1244 helix: 2.53 (0.18), residues: 805 sheet: -1.16 (0.56), residues: 68 loop : -0.65 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.012 0.001 TYR B 66 PHE 0.009 0.001 PHE F 67 TRP 0.012 0.001 TRP K 373 HIS 0.025 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00360 (17181) covalent geometry : angle 0.53771 (24477) hydrogen bonds : bond 0.04274 ( 735) hydrogen bonds : angle 3.41009 ( 2045) *********************** 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 215 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9047 (mttp) cc_final: 0.8707 (mttm) REVERT: A 70 GLU cc_start: 0.8821 (tp30) cc_final: 0.8443 (tp30) REVERT: A 73 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 81 ASP cc_start: 0.9029 (m-30) cc_final: 0.8557 (t0) REVERT: A 83 LYS cc_start: 0.9386 (mptt) cc_final: 0.9161 (mppt) REVERT: A 99 ASP cc_start: 0.8777 (t0) cc_final: 0.8422 (t0) REVERT: B 28 MET cc_start: 0.8685 (ppp) cc_final: 0.8438 (ppp) REVERT: B 41 ARG cc_start: 0.9532 (ttp-170) cc_final: 0.9134 (ttp80) REVERT: B 73 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8611 (tp30) REVERT: B 99 ASP cc_start: 0.8787 (t0) cc_final: 0.8261 (t0) REVERT: B 101 GLU cc_start: 0.8243 (pm20) cc_final: 0.7890 (pm20) REVERT: C 88 ASP cc_start: 0.8975 (t0) cc_final: 0.8708 (t0) REVERT: C 91 GLU cc_start: 0.8834 (tt0) cc_final: 0.8576 (tp30) REVERT: C 96 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 113 GLU cc_start: 0.8898 (mp0) cc_final: 0.8085 (mp0) REVERT: D 55 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8640 (tp30) REVERT: D 57 TYR cc_start: 0.9393 (m-80) cc_final: 0.9049 (m-80) REVERT: D 88 ASP cc_start: 0.9061 (t0) cc_final: 0.8503 (t0) REVERT: D 91 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8446 (tm-30) REVERT: D 113 GLU cc_start: 0.8739 (mp0) cc_final: 0.7910 (mp0) REVERT: D 125 GLU cc_start: 0.8362 (tp30) cc_final: 0.8128 (tp30) REVERT: E 50 GLU cc_start: 0.8584 (tt0) cc_final: 0.7915 (tt0) REVERT: E 115 LYS cc_start: 0.9364 (mttm) cc_final: 0.9102 (mptt) REVERT: E 133 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8490 (pt0) REVERT: E 134 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7781 (mmm160) REVERT: G 59 LYS cc_start: 0.8892 (tttt) cc_final: 0.8655 (tttm) REVERT: G 100 PHE cc_start: 0.8952 (m-80) cc_final: 0.8691 (m-80) REVERT: H 79 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8640 (mmtp) REVERT: K 296 MET cc_start: 0.8987 (ppp) cc_final: 0.8616 (ppp) REVERT: K 354 MET cc_start: 0.8729 (pmm) cc_final: 0.8220 (pmm) REVERT: K 373 TRP cc_start: 0.9231 (t60) cc_final: 0.8953 (t60) REVERT: K 452 MET cc_start: 0.8103 (ttp) cc_final: 0.7563 (ttt) REVERT: K 626 MET cc_start: 0.9083 (tpp) cc_final: 0.8586 (tpp) REVERT: K 758 MET cc_start: 0.5202 (tpt) cc_final: 0.4756 (mmm) outliers start: 18 outliers final: 16 residues processed: 206 average time/residue: 0.1219 time to fit residues: 36.9596 Evaluate side-chains 200 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 59 ILE 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 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 97 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 267 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.086358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055486 restraints weight = 55893.691| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.85 r_work: 0.2809 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4678 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= 0.223 Angle : 0.573 9.530 24477 Z= 0.325 Chirality : 0.036 0.134 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.421 159.322 4678 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.03 % Allowed : 17.80 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.24), residues: 1244 helix: 2.60 (0.18), residues: 803 sheet: -1.38 (0.52), residues: 78 loop : -0.64 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.015 0.002 TYR C 103 PHE 0.010 0.001 PHE G 100 TRP 0.013 0.001 TRP K 373 HIS 0.027 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00497 (17181) covalent geometry : angle 0.57271 (24477) hydrogen bonds : bond 0.05043 ( 735) hydrogen bonds : angle 3.55274 ( 2045) *********************** 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 214 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8939 (mttp) cc_final: 0.8675 (mttp) REVERT: A 70 GLU cc_start: 0.8869 (tp30) cc_final: 0.8417 (tp30) REVERT: A 73 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8742 (tm-30) REVERT: A 81 ASP cc_start: 0.9005 (m-30) cc_final: 0.8711 (t0) REVERT: A 98 ASN cc_start: 0.9486 (m-40) cc_final: 0.9284 (m-40) REVERT: A 99 ASP cc_start: 0.8952 (t0) cc_final: 0.8377 (t0) REVERT: B 41 ARG cc_start: 0.9563 (ttp-170) cc_final: 0.9261 (ttp80) REVERT: B 73 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8365 (tp30) REVERT: B 99 ASP cc_start: 0.8860 (t0) cc_final: 0.8289 (t0) REVERT: B 101 GLU cc_start: 0.8352 (pm20) cc_final: 0.7927 (pm20) REVERT: C 88 ASP cc_start: 0.8995 (t0) cc_final: 0.8729 (t0) REVERT: C 91 GLU cc_start: 0.8854 (tt0) cc_final: 0.8608 (tp30) REVERT: C 96 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8330 (mm-30) REVERT: C 113 GLU cc_start: 0.8861 (mp0) cc_final: 0.8014 (mp0) REVERT: D 57 TYR cc_start: 0.9410 (m-80) cc_final: 0.8985 (m-80) REVERT: D 88 ASP cc_start: 0.9085 (t0) cc_final: 0.8542 (t0) REVERT: D 91 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8463 (tm-30) REVERT: D 125 GLU cc_start: 0.8450 (tp30) cc_final: 0.8157 (tp30) REVERT: E 50 GLU cc_start: 0.8599 (tt0) cc_final: 0.7942 (tt0) REVERT: E 115 LYS cc_start: 0.9412 (mttm) cc_final: 0.9176 (mmtt) REVERT: F 50 GLU cc_start: 0.9181 (tt0) cc_final: 0.8609 (tt0) REVERT: G 59 LYS cc_start: 0.8941 (tttt) cc_final: 0.8700 (tttm) REVERT: H 44 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8692 (mtpt) REVERT: H 79 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8665 (mmtp) REVERT: K 354 MET cc_start: 0.8664 (pmm) cc_final: 0.8063 (pmm) REVERT: K 373 TRP cc_start: 0.9231 (t60) cc_final: 0.8922 (t60) REVERT: K 452 MET cc_start: 0.8242 (ttp) cc_final: 0.7848 (ttt) REVERT: K 626 MET cc_start: 0.9120 (tpp) cc_final: 0.8858 (tpp) REVERT: K 758 MET cc_start: 0.5202 (tpt) cc_final: 0.4748 (mmm) outliers start: 22 outliers final: 16 residues processed: 205 average time/residue: 0.1273 time to fit residues: 38.4118 Evaluate side-chains 201 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 143 SER 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 44 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS H 25 ASN ** 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** K 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.086236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055474 restraints weight = 56015.408| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.88 r_work: 0.2810 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4925 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= 0.210 Angle : 0.561 6.228 24477 Z= 0.319 Chirality : 0.035 0.141 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.388 162.188 4678 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.94 % Allowed : 18.17 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.24), residues: 1244 helix: 2.64 (0.18), residues: 809 sheet: -1.38 (0.53), residues: 78 loop : -0.63 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 86 TYR 0.042 0.002 TYR C 103 PHE 0.010 0.001 PHE F 67 TRP 0.012 0.001 TRP K 373 HIS 0.028 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00467 (17181) covalent geometry : angle 0.56080 (24477) hydrogen bonds : bond 0.04594 ( 735) hydrogen bonds : angle 3.46774 ( 2045) *********************** 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 208 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9026 (mttp) cc_final: 0.8341 (mttp) REVERT: A 70 GLU cc_start: 0.8872 (tp30) cc_final: 0.8331 (tp30) REVERT: A 81 ASP cc_start: 0.9040 (m-30) cc_final: 0.8657 (t0) REVERT: A 99 ASP cc_start: 0.8919 (t0) cc_final: 0.8291 (t0) REVERT: B 28 MET cc_start: 0.8679 (ppp) cc_final: 0.8467 (ppp) REVERT: B 41 ARG cc_start: 0.9558 (ttp-170) cc_final: 0.9200 (ttp80) REVERT: B 73 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8326 (tp30) REVERT: B 99 ASP cc_start: 0.8850 (t0) cc_final: 0.8213 (t0) REVERT: B 101 GLU cc_start: 0.8371 (pm20) cc_final: 0.8032 (pm20) REVERT: C 88 ASP cc_start: 0.9002 (t0) cc_final: 0.8735 (t0) REVERT: C 91 GLU cc_start: 0.8868 (tt0) cc_final: 0.8608 (tp30) REVERT: C 96 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 113 GLU cc_start: 0.8884 (mp0) cc_final: 0.8002 (mp0) REVERT: D 57 TYR cc_start: 0.9446 (m-80) cc_final: 0.8948 (m-80) REVERT: D 88 ASP cc_start: 0.9080 (t0) cc_final: 0.8649 (t0) REVERT: D 91 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 113 GLU cc_start: 0.8779 (mp0) cc_final: 0.8240 (mp0) REVERT: D 125 GLU cc_start: 0.8497 (tp30) cc_final: 0.8218 (tp30) REVERT: E 50 GLU cc_start: 0.8628 (tt0) cc_final: 0.7980 (tt0) REVERT: E 115 LYS cc_start: 0.9402 (mttm) cc_final: 0.9151 (mptt) REVERT: F 50 GLU cc_start: 0.9190 (tt0) cc_final: 0.8963 (tt0) REVERT: G 53 GLU cc_start: 0.8943 (tp30) cc_final: 0.8636 (tp30) REVERT: G 59 LYS cc_start: 0.8913 (tttt) cc_final: 0.8693 (tttm) REVERT: H 79 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8700 (mmtp) REVERT: H 98 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8221 (m-10) REVERT: K 296 MET cc_start: 0.8933 (ppp) cc_final: 0.8621 (ppp) REVERT: K 354 MET cc_start: 0.8732 (pmm) cc_final: 0.8097 (pmm) REVERT: K 373 TRP cc_start: 0.9165 (t60) cc_final: 0.8877 (t60) REVERT: K 452 MET cc_start: 0.8133 (ttp) cc_final: 0.7786 (ttt) REVERT: K 626 MET cc_start: 0.9123 (tpp) cc_final: 0.8850 (tpp) REVERT: K 758 MET cc_start: 0.5164 (tpt) cc_final: 0.4728 (mmm) outliers start: 21 outliers final: 16 residues processed: 199 average time/residue: 0.1315 time to fit residues: 38.2372 Evaluate side-chains 196 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 44 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS F 39 HIS ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 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 = 0.3798 r_free = 0.3798 target = 0.084755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053839 restraints weight = 56043.604| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.90 r_work: 0.2769 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17181 Z= 0.276 Angle : 0.616 10.704 24477 Z= 0.346 Chirality : 0.037 0.149 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.735 166.561 4678 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.03 % Allowed : 19.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.24), residues: 1244 helix: 2.54 (0.18), residues: 809 sheet: -1.53 (0.52), residues: 78 loop : -0.64 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.015 0.002 TYR B 48 PHE 0.012 0.001 PHE G 100 TRP 0.013 0.002 TRP K 373 HIS 0.030 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00617 (17181) covalent geometry : angle 0.61630 (24477) hydrogen bonds : bond 0.05528 ( 735) hydrogen bonds : angle 3.67442 ( 2045) *********************** 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: 22 poor density : 181 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8836 (tp30) cc_final: 0.8396 (tp30) REVERT: A 99 ASP cc_start: 0.8982 (t0) cc_final: 0.8358 (t0) REVERT: B 41 ARG cc_start: 0.9573 (ttp-170) cc_final: 0.9147 (ttp80) REVERT: B 70 GLU cc_start: 0.9004 (tp30) cc_final: 0.8769 (tp30) REVERT: B 73 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8501 (tp30) REVERT: B 99 ASP cc_start: 0.8827 (t0) cc_final: 0.7979 (t0) REVERT: B 101 GLU cc_start: 0.8262 (pm20) cc_final: 0.8010 (pm20) REVERT: C 88 ASP cc_start: 0.9017 (t0) cc_final: 0.8765 (t0) REVERT: C 91 GLU cc_start: 0.8878 (tt0) cc_final: 0.8640 (tp30) REVERT: C 96 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 103 TYR cc_start: 0.7705 (m-10) cc_final: 0.7493 (m-80) REVERT: C 113 GLU cc_start: 0.8908 (mp0) cc_final: 0.8057 (mp0) REVERT: C 129 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8836 (m170) REVERT: D 53 ASN cc_start: 0.8499 (m-40) cc_final: 0.8087 (t0) REVERT: D 55 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8384 (tp30) REVERT: D 57 TYR cc_start: 0.9469 (m-80) cc_final: 0.8999 (m-80) REVERT: D 88 ASP cc_start: 0.9094 (t0) cc_final: 0.8645 (t0) REVERT: D 91 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8486 (tm-30) REVERT: D 113 GLU cc_start: 0.8778 (mp0) cc_final: 0.8227 (mp0) REVERT: D 125 GLU cc_start: 0.8512 (tp30) cc_final: 0.8252 (tp30) REVERT: E 50 GLU cc_start: 0.8730 (tt0) cc_final: 0.8056 (tt0) REVERT: E 115 LYS cc_start: 0.9451 (mttm) cc_final: 0.9225 (mmtt) REVERT: F 50 GLU cc_start: 0.9231 (tt0) cc_final: 0.9023 (tt0) REVERT: G 53 GLU cc_start: 0.9027 (tp30) cc_final: 0.8722 (tp30) REVERT: G 59 LYS cc_start: 0.8955 (tttt) cc_final: 0.8707 (tttm) REVERT: H 44 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8885 (mtpt) REVERT: H 79 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8967 (mmtm) REVERT: H 98 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: K 354 MET cc_start: 0.8778 (pmm) cc_final: 0.8093 (pmm) REVERT: K 452 MET cc_start: 0.8098 (ttp) cc_final: 0.7838 (ttt) REVERT: K 626 MET cc_start: 0.9163 (tpp) cc_final: 0.8927 (tpp) REVERT: K 758 MET cc_start: 0.5550 (tpt) cc_final: 0.5135 (mmm) outliers start: 22 outliers final: 18 residues processed: 195 average time/residue: 0.1227 time to fit residues: 35.5164 Evaluate side-chains 200 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL 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 86 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER 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 44 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS H 18 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 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 = 0.3814 r_free = 0.3814 target = 0.085619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055023 restraints weight = 56117.702| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.88 r_work: 0.2804 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5375 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= 0.196 Angle : 0.571 9.879 24477 Z= 0.323 Chirality : 0.035 0.155 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.589 170.223 4678 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.03 % Allowed : 19.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.24), residues: 1244 helix: 2.64 (0.18), residues: 809 sheet: -1.45 (0.52), residues: 78 loop : -0.60 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 86 TYR 0.014 0.001 TYR C 103 PHE 0.010 0.001 PHE F 67 TRP 0.012 0.001 TRP K 373 HIS 0.008 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00434 (17181) covalent geometry : angle 0.57064 (24477) hydrogen bonds : bond 0.04574 ( 735) hydrogen bonds : angle 3.41113 ( 2045) *********************** 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 207 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9065 (mttp) cc_final: 0.8802 (mttp) REVERT: A 70 GLU cc_start: 0.8814 (tp30) cc_final: 0.8468 (tp30) REVERT: A 99 ASP cc_start: 0.8951 (t0) cc_final: 0.8289 (t0) REVERT: B 41 ARG cc_start: 0.9563 (ttp-170) cc_final: 0.9140 (ttp80) REVERT: B 70 GLU cc_start: 0.8959 (tp30) cc_final: 0.8706 (tp30) REVERT: B 73 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8359 (tp30) REVERT: B 99 ASP cc_start: 0.8855 (t0) cc_final: 0.7954 (t0) REVERT: C 88 ASP cc_start: 0.8987 (t0) cc_final: 0.8721 (t0) REVERT: C 91 GLU cc_start: 0.8860 (tt0) cc_final: 0.8616 (tp30) REVERT: C 96 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8360 (mm-30) REVERT: C 113 GLU cc_start: 0.8873 (mp0) cc_final: 0.8014 (mp0) REVERT: D 55 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8590 (tp30) REVERT: D 57 TYR cc_start: 0.9459 (m-80) cc_final: 0.9034 (m-80) REVERT: D 88 ASP cc_start: 0.9082 (t0) cc_final: 0.8637 (t0) REVERT: D 91 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 113 GLU cc_start: 0.8762 (mp0) cc_final: 0.8256 (mp0) REVERT: D 125 GLU cc_start: 0.8450 (tp30) cc_final: 0.8186 (tp30) REVERT: E 50 GLU cc_start: 0.8665 (tt0) cc_final: 0.8012 (tt0) REVERT: E 115 LYS cc_start: 0.9473 (mttm) cc_final: 0.9212 (mptt) REVERT: E 134 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7806 (mmm160) REVERT: F 50 GLU cc_start: 0.9215 (tt0) cc_final: 0.8975 (tt0) REVERT: G 53 GLU cc_start: 0.8909 (tp30) cc_final: 0.8603 (tp30) REVERT: G 59 LYS cc_start: 0.8928 (tttt) cc_final: 0.8712 (tttm) REVERT: H 98 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8263 (m-10) REVERT: K 354 MET cc_start: 0.8713 (pmm) cc_final: 0.8057 (pmm) REVERT: K 373 TRP cc_start: 0.9152 (t60) cc_final: 0.8842 (t60) REVERT: K 452 MET cc_start: 0.8067 (ttp) cc_final: 0.7645 (ttt) REVERT: K 626 MET cc_start: 0.9093 (tpp) cc_final: 0.8829 (tpp) REVERT: K 758 MET cc_start: 0.5431 (tpt) cc_final: 0.5047 (mmm) outliers start: 22 outliers final: 18 residues processed: 198 average time/residue: 0.1245 time to fit residues: 36.8064 Evaluate side-chains 198 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL 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 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 44 LYS Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 499 HIS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS F 39 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 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 = 0.3816 r_free = 0.3816 target = 0.085682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055097 restraints weight = 56575.129| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.87 r_work: 0.2805 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.044 17181 Z= 0.200 Angle : 0.588 12.701 24477 Z= 0.328 Chirality : 0.035 0.149 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.608 174.894 4678 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.85 % Allowed : 20.30 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.24), residues: 1244 helix: 2.67 (0.18), residues: 809 sheet: -1.41 (0.53), residues: 78 loop : -0.57 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.018 0.002 TYR C 103 PHE 0.010 0.001 PHE F 67 TRP 0.012 0.001 TRP K 373 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00444 (17181) covalent geometry : angle 0.58793 (24477) hydrogen bonds : bond 0.04722 ( 735) hydrogen bonds : angle 3.42776 ( 2045) *********************** 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 204 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8920 (tp30) cc_final: 0.8474 (tp30) REVERT: A 99 ASP cc_start: 0.8947 (t0) cc_final: 0.8286 (t0) REVERT: B 41 ARG cc_start: 0.9564 (ttp-170) cc_final: 0.9087 (ttp80) REVERT: B 73 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8343 (tp30) REVERT: B 99 ASP cc_start: 0.8802 (t0) cc_final: 0.8175 (t0) REVERT: C 88 ASP cc_start: 0.8997 (t0) cc_final: 0.8733 (t0) REVERT: C 91 GLU cc_start: 0.8880 (tt0) cc_final: 0.8629 (tp30) REVERT: C 96 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8344 (mm-30) REVERT: C 113 GLU cc_start: 0.8880 (mp0) cc_final: 0.7971 (mp0) REVERT: D 55 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8344 (tp30) REVERT: D 57 TYR cc_start: 0.9455 (m-80) cc_final: 0.9037 (m-80) REVERT: D 88 ASP cc_start: 0.9094 (t0) cc_final: 0.8657 (t0) REVERT: D 91 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 113 GLU cc_start: 0.8749 (mp0) cc_final: 0.8097 (mp0) REVERT: D 125 GLU cc_start: 0.8437 (tp30) cc_final: 0.8162 (tp30) REVERT: E 50 GLU cc_start: 0.8687 (tt0) cc_final: 0.8036 (tt0) REVERT: E 115 LYS cc_start: 0.9484 (mttm) cc_final: 0.9234 (mptt) REVERT: E 134 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7839 (mmm160) REVERT: F 50 GLU cc_start: 0.9199 (tt0) cc_final: 0.8957 (tt0) REVERT: G 53 GLU cc_start: 0.8907 (tp30) cc_final: 0.8603 (tp30) REVERT: G 59 LYS cc_start: 0.8957 (tttt) cc_final: 0.8747 (tttm) REVERT: H 98 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: K 296 MET cc_start: 0.8739 (ppp) cc_final: 0.8357 (ppp) REVERT: K 354 MET cc_start: 0.8737 (pmm) cc_final: 0.8027 (pmm) REVERT: K 373 TRP cc_start: 0.9199 (t60) cc_final: 0.8889 (t60) REVERT: K 452 MET cc_start: 0.8006 (ttp) cc_final: 0.7595 (ttt) REVERT: K 626 MET cc_start: 0.9127 (tpp) cc_final: 0.8597 (tpp) REVERT: K 758 MET cc_start: 0.5456 (tpt) cc_final: 0.5065 (mmm) outliers start: 20 outliers final: 17 residues processed: 196 average time/residue: 0.1420 time to fit residues: 41.2540 Evaluate side-chains 199 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL 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 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 499 HIS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE 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 116 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 456 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 = 0.3837 r_free = 0.3837 target = 0.086909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056154 restraints weight = 56021.732| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.92 r_work: 0.2847 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.5520 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= 0.149 Angle : 0.566 11.373 24477 Z= 0.317 Chirality : 0.034 0.177 2776 Planarity : 0.004 0.045 2050 Dihedral : 29.417 176.102 4678 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.20 % Allowed : 20.94 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.24), residues: 1244 helix: 2.77 (0.18), residues: 802 sheet: -1.34 (0.52), residues: 78 loop : -0.48 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.020 0.001 TYR C 103 PHE 0.008 0.001 PHE F 67 TRP 0.010 0.001 TRP K 373 HIS 0.006 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00324 (17181) covalent geometry : angle 0.56600 (24477) hydrogen bonds : bond 0.04157 ( 735) hydrogen bonds : angle 3.24357 ( 2045) ********************** 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 208 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9092 (mttp) cc_final: 0.8677 (mttm) REVERT: A 70 GLU cc_start: 0.8911 (tp30) cc_final: 0.8475 (tp30) REVERT: A 83 LYS cc_start: 0.9248 (mppt) cc_final: 0.9024 (mppt) REVERT: A 99 ASP cc_start: 0.8932 (t0) cc_final: 0.8210 (t0) REVERT: B 41 ARG cc_start: 0.9516 (ttp-170) cc_final: 0.9138 (ttp80) REVERT: B 73 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8272 (tp30) REVERT: B 99 ASP cc_start: 0.8741 (t0) cc_final: 0.8082 (t0) REVERT: C 88 ASP cc_start: 0.8973 (t0) cc_final: 0.8709 (t0) REVERT: C 91 GLU cc_start: 0.8837 (tt0) cc_final: 0.8616 (tp30) REVERT: C 96 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8353 (mm-30) REVERT: C 113 GLU cc_start: 0.8937 (mp0) cc_final: 0.8054 (mp0) REVERT: D 55 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8377 (tp30) REVERT: D 57 TYR cc_start: 0.9435 (m-80) cc_final: 0.9032 (m-80) REVERT: D 88 ASP cc_start: 0.9072 (t0) cc_final: 0.8515 (t0) REVERT: D 91 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8522 (tm-30) REVERT: D 113 GLU cc_start: 0.8772 (mp0) cc_final: 0.8086 (mp0) REVERT: D 125 GLU cc_start: 0.8353 (tp30) cc_final: 0.8097 (tp30) REVERT: E 50 GLU cc_start: 0.8635 (tt0) cc_final: 0.7973 (tt0) REVERT: E 115 LYS cc_start: 0.9452 (mttm) cc_final: 0.9205 (mptt) REVERT: E 134 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7990 (mmm160) REVERT: F 50 GLU cc_start: 0.9217 (tt0) cc_final: 0.8947 (tt0) REVERT: G 84 MET cc_start: 0.8848 (tpp) cc_final: 0.8401 (mmm) REVERT: K 296 MET cc_start: 0.8768 (ppp) cc_final: 0.8500 (ppp) REVERT: K 354 MET cc_start: 0.8707 (pmm) cc_final: 0.7990 (pmm) REVERT: K 373 TRP cc_start: 0.9200 (t60) cc_final: 0.8911 (t60) REVERT: K 452 MET cc_start: 0.7993 (ttp) cc_final: 0.7418 (ttt) REVERT: K 626 MET cc_start: 0.9101 (tpp) cc_final: 0.8568 (tpp) outliers start: 13 outliers final: 11 residues processed: 203 average time/residue: 0.1373 time to fit residues: 41.5972 Evaluate side-chains 195 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 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 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 499 HIS 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 49 optimal weight: 0.3980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS F 39 HIS G 93 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.085896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054973 restraints weight = 56222.264| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.90 r_work: 0.2820 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17181 Z= 0.190 Angle : 0.583 11.650 24477 Z= 0.324 Chirality : 0.035 0.173 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.521 176.576 4678 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.11 % Allowed : 20.85 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.24), residues: 1244 helix: 2.68 (0.18), residues: 809 sheet: -1.28 (0.53), residues: 78 loop : -0.49 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 86 TYR 0.019 0.002 TYR C 103 PHE 0.009 0.001 PHE F 67 TRP 0.012 0.001 TRP K 373 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00423 (17181) covalent geometry : angle 0.58348 (24477) hydrogen bonds : bond 0.04584 ( 735) hydrogen bonds : angle 3.36146 ( 2045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4570.97 seconds wall clock time: 78 minutes 40.06 seconds (4720.06 seconds total)