Starting phenix.real_space_refine on Sat May 17 20:31:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcc_37099/05_2025/8kcc_37099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcc_37099/05_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_37099/05_2025/8kcc_37099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcc_37099/05_2025/8kcc_37099.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcc_37099/05_2025/8kcc_37099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcc_37099/05_2025/8kcc_37099.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 302 5.49 5 S 34 5.16 5 Be 1 3.05 5 C 9342 2.51 5 N 2986 2.21 5 O 3603 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16271 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "C" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 719 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3053 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3097 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4088 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 487} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.32, per 1000 atoms: 0.63 Number of scatterers: 16271 At special positions: 0 Unit cell: (134.734, 100.05, 142.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 P 302 15.00 F 3 9.00 O 3603 8.00 N 2986 7.00 C 9342 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 65.4% alpha, 6.9% beta 60 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.557A pdb=" N ILE A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 82 removed outlier: 4.416A pdb=" N VAL A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.689A pdb=" N ILE B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 82 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 75 through 104 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 124 through 144 Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 75 through 104 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 144 Processing helix chain 'E' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.528A pdb=" N ILE G 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.732A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 48 through 76 removed outlier: 4.479A pdb=" N GLU H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.531A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 Processing helix chain 'K' and resid 203 through 220 Processing helix chain 'K' and resid 232 through 247 removed outlier: 3.885A pdb=" N GLN K 236 " --> pdb=" O GLY K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 272 removed outlier: 4.188A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 Processing helix chain 'K' and resid 310 through 318 Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.591A pdb=" N ARG K 347 " --> pdb=" O CYS K 343 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 380 removed outlier: 3.932A pdb=" N SER K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 375 " --> pdb=" O GLU K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 394 removed outlier: 3.739A pdb=" N PHE K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 424 Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 472 Processing helix chain 'K' and resid 489 through 498 Processing helix chain 'K' and resid 499 through 509 removed outlier: 3.905A pdb=" N LEU K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 523 removed outlier: 4.401A pdb=" N CYS K 523 " --> pdb=" O ILE K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 540 Processing helix chain 'K' and resid 549 through 564 removed outlier: 3.599A pdb=" N LEU K 553 " --> pdb=" O TRP K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 623 through 632 removed outlier: 3.749A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 671 removed outlier: 4.001A pdb=" N LEU K 668 " --> pdb=" O SER K 664 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 669 " --> pdb=" O LYS K 665 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 711 removed outlier: 3.595A pdb=" N THR K 711 " --> pdb=" O LYS K 707 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 723 removed outlier: 3.791A pdb=" N ASP K 723 " --> pdb=" O ASP K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.970A pdb=" N ARG A 51 " --> pdb=" O ILE D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 52 removed outlier: 7.245A pdb=" N ARG B 51 " --> pdb=" O ILE C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.934A pdb=" N THR B 110 " --> pdb=" O TYR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.144A pdb=" N ARG E 83 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'F' and resid 83 through 84 removed outlier: 7.331A pdb=" N ARG F 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'K' and resid 224 through 225 removed outlier: 7.153A pdb=" N ILE K 224 " --> pdb=" O LEU K 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N TRP K 327 " --> pdb=" O ASP K 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU K 360 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE K 332 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.036A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER K 599 " --> pdb=" O CYS K 568 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE K 570 " --> pdb=" O SER K 599 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL K 543 " --> pdb=" O PHE K 596 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU K 598 " --> pdb=" O VAL K 543 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE K 545 " --> pdb=" O LEU K 598 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 4.52 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.500 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 17181 Z= 0.220 Angle : 0.550 12.768 24477 Z= 0.323 Chirality : 0.033 0.231 2776 Planarity : 0.003 0.032 2050 Dihedral : 25.142 151.222 7207 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.20 % Allowed : 1.75 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1244 helix: 0.77 (0.17), residues: 798 sheet: -1.70 (0.56), residues: 66 loop : -1.34 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 212 HIS 0.010 0.001 HIS K 670 PHE 0.012 0.001 PHE K 459 TYR 0.008 0.001 TYR B 66 ARG 0.003 0.000 ARG H 17 Details of bonding type rmsd hydrogen bonds : bond 0.17466 ( 735) hydrogen bonds : angle 6.49654 ( 2045) covalent geometry : bond 0.00433 (17181) covalent geometry : angle 0.55008 (24477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 1.508 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: 0.3460 time to fit residues: 138.4431 Evaluate side-chains 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain H residue 17 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN C 69 HIS D 69 HIS D 115 GLN E 39 HIS E 68 GLN E 113 HIS F 85 GLN F 93 GLN H 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 HIS K 336 HIS ** K 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 639 GLN K 644 HIS K 710 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.088748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057142 restraints weight = 56054.300| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.97 r_work: 0.2827 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17181 Z= 0.334 Angle : 0.705 10.571 24477 Z= 0.392 Chirality : 0.043 0.200 2776 Planarity : 0.005 0.053 2050 Dihedral : 29.550 151.905 4685 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.77 % Allowed : 12.36 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1244 helix: 1.90 (0.18), residues: 803 sheet: -1.38 (0.57), residues: 68 loop : -0.97 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 748 HIS 0.012 0.002 HIS H 18 PHE 0.038 0.002 PHE F 41 TYR 0.017 0.002 TYR K 513 ARG 0.006 0.001 ARG K 431 Details of bonding type rmsd hydrogen bonds : bond 0.06855 ( 735) hydrogen bonds : angle 4.03921 ( 2045) covalent geometry : bond 0.00748 (17181) covalent geometry : angle 0.70507 (24477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9133 (mttp) cc_final: 0.8775 (mttp) REVERT: A 44 LYS cc_start: 0.9256 (ttmm) cc_final: 0.9004 (mtpt) REVERT: A 70 GLU cc_start: 0.8880 (tp30) cc_final: 0.8505 (tp30) REVERT: A 81 ASP cc_start: 0.9037 (m-30) cc_final: 0.8659 (t0) REVERT: A 101 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8741 (mm-30) REVERT: B 73 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8289 (tp30) REVERT: B 81 ASP cc_start: 0.9169 (m-30) cc_final: 0.8959 (m-30) REVERT: B 99 ASP cc_start: 0.8836 (t0) cc_final: 0.8457 (t0) REVERT: B 101 GLU cc_start: 0.8346 (pm20) cc_final: 0.7927 (pm20) REVERT: C 82 MET cc_start: 0.9399 (mmm) cc_final: 0.8976 (tpp) REVERT: C 88 ASP cc_start: 0.9018 (t0) cc_final: 0.8762 (t0) REVERT: C 91 GLU cc_start: 0.8881 (tt0) cc_final: 0.8516 (tp30) REVERT: C 96 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 55 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8190 (mm-30) REVERT: D 88 ASP cc_start: 0.9070 (t0) cc_final: 0.8520 (t0) REVERT: D 91 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8531 (tm-30) REVERT: D 113 GLU cc_start: 0.8870 (mp0) cc_final: 0.8065 (mp0) REVERT: E 50 GLU cc_start: 0.8598 (tt0) cc_final: 0.7996 (tt0) REVERT: E 115 LYS cc_start: 0.9433 (mttm) cc_final: 0.9230 (mmtt) REVERT: E 134 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7878 (mmm160) REVERT: F 53 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8797 (ttpp) REVERT: G 59 LYS cc_start: 0.8990 (tttt) cc_final: 0.8692 (tttm) REVERT: G 100 PHE cc_start: 0.8875 (m-80) cc_final: 0.8592 (m-80) REVERT: H 27 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8795 (mm-40) REVERT: H 79 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8792 (mmtp) REVERT: K 284 ASP cc_start: 0.8663 (t70) cc_final: 0.8355 (t70) REVERT: K 296 MET cc_start: 0.8738 (ppp) cc_final: 0.8414 (ppp) REVERT: K 354 MET cc_start: 0.9037 (pmm) cc_final: 0.8577 (pmm) REVERT: K 452 MET cc_start: 0.8216 (ttp) cc_final: 0.7646 (ttt) REVERT: K 454 ASP cc_start: 0.9375 (p0) cc_final: 0.9020 (t0) REVERT: K 502 LEU cc_start: 0.8520 (tp) cc_final: 0.8140 (tp) REVERT: K 556 MET cc_start: 0.9375 (mtm) cc_final: 0.8480 (ptp) REVERT: K 758 MET cc_start: 0.5320 (tpt) cc_final: 0.4754 (tpp) outliers start: 30 outliers final: 22 residues processed: 223 average time/residue: 0.2991 time to fit residues: 96.2516 Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 343 CYS Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058289 restraints weight = 54906.121| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.85 r_work: 0.2868 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17181 Z= 0.180 Angle : 0.550 7.659 24477 Z= 0.314 Chirality : 0.035 0.156 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.253 155.410 4678 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.20 % Allowed : 15.31 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1244 helix: 2.34 (0.18), residues: 804 sheet: -1.29 (0.56), residues: 68 loop : -0.84 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.007 0.001 HIS K 336 PHE 0.014 0.001 PHE E 41 TYR 0.013 0.001 TYR K 513 ARG 0.005 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 735) hydrogen bonds : angle 3.47751 ( 2045) covalent geometry : bond 0.00400 (17181) covalent geometry : angle 0.55033 (24477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.9292 (tmm) cc_final: 0.8878 (tmm) REVERT: A 70 GLU cc_start: 0.8883 (tp30) cc_final: 0.8430 (tp30) REVERT: A 73 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8702 (tm-30) REVERT: A 81 ASP cc_start: 0.9010 (m-30) cc_final: 0.8708 (t0) REVERT: A 99 ASP cc_start: 0.8749 (t0) cc_final: 0.8411 (t0) REVERT: B 41 ARG cc_start: 0.9597 (ttp-170) cc_final: 0.9257 (ttp80) REVERT: B 73 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8637 (tp30) REVERT: B 99 ASP cc_start: 0.8752 (t0) cc_final: 0.8290 (t0) REVERT: B 101 GLU cc_start: 0.8210 (pm20) cc_final: 0.7831 (pm20) REVERT: C 88 ASP cc_start: 0.8980 (t0) cc_final: 0.8717 (t0) REVERT: C 91 GLU cc_start: 0.8799 (tt0) cc_final: 0.8542 (tp30) REVERT: C 96 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8347 (mm-30) REVERT: C 113 GLU cc_start: 0.8819 (mp0) cc_final: 0.8028 (mp0) REVERT: D 57 TYR cc_start: 0.9399 (m-80) cc_final: 0.9096 (m-80) REVERT: D 88 ASP cc_start: 0.9052 (t0) cc_final: 0.8492 (t0) REVERT: D 91 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 113 GLU cc_start: 0.8786 (mp0) cc_final: 0.7986 (mp0) REVERT: E 50 GLU cc_start: 0.8595 (tt0) cc_final: 0.7914 (tt0) REVERT: E 115 LYS cc_start: 0.9364 (mttm) cc_final: 0.9116 (mmtm) REVERT: F 50 GLU cc_start: 0.9189 (tt0) cc_final: 0.8959 (tt0) REVERT: G 53 GLU cc_start: 0.8881 (tp30) cc_final: 0.8596 (tp30) REVERT: G 59 LYS cc_start: 0.8869 (tttt) cc_final: 0.8611 (tttm) REVERT: G 100 PHE cc_start: 0.8840 (m-80) cc_final: 0.8574 (m-80) REVERT: H 27 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8747 (mm-40) REVERT: H 79 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8777 (mmtp) REVERT: K 296 MET cc_start: 0.8955 (ppp) cc_final: 0.8624 (ppp) REVERT: K 344 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8696 (mmtp) REVERT: K 354 MET cc_start: 0.8790 (pmm) cc_final: 0.8433 (pmm) REVERT: K 373 TRP cc_start: 0.9213 (t60) cc_final: 0.8918 (t60) REVERT: K 452 MET cc_start: 0.8144 (ttp) cc_final: 0.7474 (ttt) REVERT: K 556 MET cc_start: 0.9322 (mtm) cc_final: 0.8446 (ptp) REVERT: K 758 MET cc_start: 0.5240 (tpt) cc_final: 0.4799 (mmm) outliers start: 13 outliers final: 11 residues processed: 204 average time/residue: 0.2808 time to fit residues: 85.1477 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 : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS 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 143 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 chunk 123 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.089088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058093 restraints weight = 56059.481| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.90 r_work: 0.2868 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3966 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= 0.169 Angle : 0.534 8.448 24477 Z= 0.305 Chirality : 0.034 0.139 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.142 157.344 4678 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.85 % Allowed : 15.41 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.24), residues: 1244 helix: 2.60 (0.18), residues: 804 sheet: -1.19 (0.56), residues: 68 loop : -0.69 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.025 0.001 HIS K 499 PHE 0.011 0.001 PHE F 78 TYR 0.012 0.001 TYR B 66 ARG 0.006 0.000 ARG F 69 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 735) hydrogen bonds : angle 3.35578 ( 2045) covalent geometry : bond 0.00370 (17181) covalent geometry : angle 0.53358 (24477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9161 (mttp) cc_final: 0.8700 (mttp) REVERT: A 70 GLU cc_start: 0.8864 (tp30) cc_final: 0.8438 (tp30) REVERT: A 73 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8745 (tm-30) REVERT: A 81 ASP cc_start: 0.9008 (m-30) cc_final: 0.8533 (t0) REVERT: A 83 LYS cc_start: 0.9353 (mptt) cc_final: 0.9140 (mppt) REVERT: A 99 ASP cc_start: 0.8902 (t0) cc_final: 0.8298 (t0) REVERT: B 28 MET cc_start: 0.8710 (ppp) cc_final: 0.8458 (ppp) REVERT: B 41 ARG cc_start: 0.9555 (ttp-170) cc_final: 0.9185 (ttp80) REVERT: B 73 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8314 (tp30) REVERT: B 99 ASP cc_start: 0.8824 (t0) cc_final: 0.8229 (t0) REVERT: B 101 GLU cc_start: 0.8230 (pm20) cc_final: 0.7877 (pm20) REVERT: C 88 ASP cc_start: 0.8980 (t0) cc_final: 0.8721 (t0) REVERT: C 96 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8347 (mm-30) REVERT: C 113 GLU cc_start: 0.8895 (mp0) cc_final: 0.8077 (mp0) REVERT: D 57 TYR cc_start: 0.9388 (m-80) cc_final: 0.9085 (m-80) REVERT: D 88 ASP cc_start: 0.9075 (t0) cc_final: 0.8522 (t0) REVERT: D 91 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 113 GLU cc_start: 0.8745 (mp0) cc_final: 0.7977 (mp0) REVERT: D 125 GLU cc_start: 0.8422 (tp30) cc_final: 0.8126 (tp30) REVERT: E 50 GLU cc_start: 0.8588 (tt0) cc_final: 0.7808 (tt0) REVERT: E 54 TYR cc_start: 0.9023 (m-80) cc_final: 0.8556 (m-80) REVERT: E 115 LYS cc_start: 0.9382 (mttm) cc_final: 0.9133 (mmtt) REVERT: E 133 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8049 (pt0) REVERT: G 59 LYS cc_start: 0.8918 (tttt) cc_final: 0.8690 (tttm) REVERT: G 100 PHE cc_start: 0.8933 (m-80) cc_final: 0.8682 (m-80) REVERT: H 27 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8757 (mm-40) REVERT: H 79 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8612 (mmtp) REVERT: K 296 MET cc_start: 0.8986 (ppp) cc_final: 0.8624 (ppp) REVERT: K 354 MET cc_start: 0.8748 (pmm) cc_final: 0.8178 (pmm) REVERT: K 373 TRP cc_start: 0.9221 (t60) cc_final: 0.8947 (t60) REVERT: K 452 MET cc_start: 0.8128 (ttp) cc_final: 0.7550 (ttt) REVERT: K 499 HIS cc_start: 0.6237 (p-80) cc_final: 0.5891 (p-80) REVERT: K 502 LEU cc_start: 0.8302 (tp) cc_final: 0.7969 (tp) REVERT: K 626 MET cc_start: 0.8823 (tpp) cc_final: 0.8553 (mmt) REVERT: K 758 MET cc_start: 0.5241 (tpt) cc_final: 0.4789 (mmm) outliers start: 20 outliers final: 15 residues processed: 205 average time/residue: 0.2909 time to fit residues: 87.6623 Evaluate side-chains 197 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 43 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.087721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057079 restraints weight = 55743.156| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.84 r_work: 0.2846 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4441 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= 0.191 Angle : 0.546 8.882 24477 Z= 0.311 Chirality : 0.034 0.132 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.278 159.516 4678 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.75 % Allowed : 17.62 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1244 helix: 2.68 (0.18), residues: 804 sheet: -1.34 (0.52), residues: 78 loop : -0.57 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.020 0.001 HIS K 499 PHE 0.009 0.001 PHE F 78 TYR 0.012 0.001 TYR B 66 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 735) hydrogen bonds : angle 3.39555 ( 2045) covalent geometry : bond 0.00422 (17181) covalent geometry : angle 0.54640 (24477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9135 (mttp) cc_final: 0.8719 (mttp) REVERT: A 47 ARG cc_start: 0.8868 (ttp-170) cc_final: 0.8407 (ptm160) REVERT: A 70 GLU cc_start: 0.8875 (tp30) cc_final: 0.8433 (tp30) REVERT: A 73 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 81 ASP cc_start: 0.9033 (m-30) cc_final: 0.8754 (t0) REVERT: A 99 ASP cc_start: 0.8992 (t0) cc_final: 0.8354 (t0) REVERT: B 41 ARG cc_start: 0.9588 (ttp-170) cc_final: 0.9223 (ttp80) REVERT: B 73 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8333 (tp30) REVERT: B 99 ASP cc_start: 0.8871 (t0) cc_final: 0.8165 (t0) REVERT: B 101 GLU cc_start: 0.8362 (pm20) cc_final: 0.8033 (pm20) REVERT: C 88 ASP cc_start: 0.8966 (t0) cc_final: 0.8720 (t0) REVERT: C 91 GLU cc_start: 0.9245 (tp30) cc_final: 0.8766 (tp30) REVERT: C 96 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8344 (mm-30) REVERT: C 113 GLU cc_start: 0.8919 (mp0) cc_final: 0.8080 (mp0) REVERT: D 57 TYR cc_start: 0.9433 (m-80) cc_final: 0.9035 (m-80) REVERT: D 88 ASP cc_start: 0.9075 (t0) cc_final: 0.8521 (t0) REVERT: D 91 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8462 (tm-30) REVERT: D 97 SER cc_start: 0.9438 (m) cc_final: 0.9224 (m) REVERT: D 113 GLU cc_start: 0.8767 (mp0) cc_final: 0.7952 (mp0) REVERT: D 125 GLU cc_start: 0.8539 (tp30) cc_final: 0.8137 (tp30) REVERT: E 50 GLU cc_start: 0.8676 (tt0) cc_final: 0.8007 (tt0) REVERT: E 115 LYS cc_start: 0.9391 (mttm) cc_final: 0.9150 (mmtt) REVERT: F 50 GLU cc_start: 0.9182 (tt0) cc_final: 0.8964 (tt0) REVERT: G 59 LYS cc_start: 0.8916 (tttt) cc_final: 0.8701 (tttm) REVERT: G 100 PHE cc_start: 0.8990 (m-80) cc_final: 0.8730 (m-80) REVERT: H 27 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8842 (mm-40) REVERT: H 79 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8639 (mmtp) REVERT: K 354 MET cc_start: 0.8603 (pmm) cc_final: 0.8072 (pmm) REVERT: K 373 TRP cc_start: 0.9231 (t60) cc_final: 0.8948 (t60) REVERT: K 452 MET cc_start: 0.8067 (ttp) cc_final: 0.7630 (ttt) REVERT: K 502 LEU cc_start: 0.8371 (tp) cc_final: 0.7817 (tp) REVERT: K 758 MET cc_start: 0.5186 (tpt) cc_final: 0.4736 (mmm) outliers start: 19 outliers final: 14 residues processed: 203 average time/residue: 0.2834 time to fit residues: 85.3118 Evaluate side-chains 196 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE 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 108 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 H 25 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.087789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.057019 restraints weight = 55498.654| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.85 r_work: 0.2850 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4657 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= 0.176 Angle : 0.540 10.109 24477 Z= 0.306 Chirality : 0.034 0.146 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.216 162.179 4678 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.85 % Allowed : 18.17 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.24), residues: 1244 helix: 2.79 (0.18), residues: 804 sheet: -1.35 (0.51), residues: 78 loop : -0.55 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 373 HIS 0.004 0.001 HIS K 499 PHE 0.008 0.001 PHE F 67 TYR 0.011 0.001 TYR B 66 ARG 0.010 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 735) hydrogen bonds : angle 3.30421 ( 2045) covalent geometry : bond 0.00389 (17181) covalent geometry : angle 0.53991 (24477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9156 (mttp) cc_final: 0.8716 (mttp) REVERT: A 70 GLU cc_start: 0.8866 (tp30) cc_final: 0.8428 (tp30) REVERT: A 73 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 81 ASP cc_start: 0.9014 (m-30) cc_final: 0.8597 (t0) REVERT: A 83 LYS cc_start: 0.9393 (mptt) cc_final: 0.9157 (mppt) REVERT: A 99 ASP cc_start: 0.8982 (t0) cc_final: 0.8290 (t0) REVERT: B 28 MET cc_start: 0.8675 (ppp) cc_final: 0.8468 (ppp) REVERT: B 41 ARG cc_start: 0.9573 (ttp-170) cc_final: 0.9201 (ttp80) REVERT: B 73 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8325 (tp30) REVERT: B 99 ASP cc_start: 0.8875 (t0) cc_final: 0.8151 (t0) REVERT: B 101 GLU cc_start: 0.8429 (pm20) cc_final: 0.8056 (pm20) REVERT: C 88 ASP cc_start: 0.8956 (t0) cc_final: 0.8709 (t0) REVERT: C 96 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 113 GLU cc_start: 0.8911 (mp0) cc_final: 0.8051 (mp0) REVERT: D 57 TYR cc_start: 0.9416 (m-80) cc_final: 0.9030 (m-80) REVERT: D 88 ASP cc_start: 0.9071 (t0) cc_final: 0.8515 (t0) REVERT: D 91 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 97 SER cc_start: 0.9443 (m) cc_final: 0.9228 (m) REVERT: D 113 GLU cc_start: 0.8739 (mp0) cc_final: 0.7910 (mp0) REVERT: D 125 GLU cc_start: 0.8512 (tp30) cc_final: 0.8127 (tp30) REVERT: E 50 GLU cc_start: 0.8647 (tt0) cc_final: 0.7991 (tt0) REVERT: E 115 LYS cc_start: 0.9396 (mttm) cc_final: 0.9151 (mptt) REVERT: G 53 GLU cc_start: 0.8879 (tp30) cc_final: 0.8596 (tp30) REVERT: G 59 LYS cc_start: 0.8928 (tttt) cc_final: 0.8724 (tttm) REVERT: G 100 PHE cc_start: 0.8990 (m-80) cc_final: 0.8712 (m-80) REVERT: H 27 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8820 (mm-40) REVERT: H 79 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8656 (mmtp) REVERT: K 296 MET cc_start: 0.8944 (ppp) cc_final: 0.8648 (ppp) REVERT: K 354 MET cc_start: 0.8635 (pmm) cc_final: 0.8041 (pmm) REVERT: K 373 TRP cc_start: 0.9171 (t60) cc_final: 0.8906 (t60) REVERT: K 452 MET cc_start: 0.8054 (ttp) cc_final: 0.7605 (ttt) REVERT: K 502 LEU cc_start: 0.7968 (tp) cc_final: 0.7675 (tp) REVERT: K 758 MET cc_start: 0.5214 (tpt) cc_final: 0.4756 (mmm) outliers start: 20 outliers final: 16 residues processed: 200 average time/residue: 0.2855 time to fit residues: 84.2673 Evaluate side-chains 198 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 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 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 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 77 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055757 restraints weight = 55597.239| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.83 r_work: 0.2823 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.5038 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= 0.201 Angle : 0.554 9.862 24477 Z= 0.315 Chirality : 0.035 0.131 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.425 166.753 4678 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.75 % Allowed : 18.17 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.24), residues: 1244 helix: 2.75 (0.18), residues: 810 sheet: -1.31 (0.52), residues: 78 loop : -0.50 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 373 HIS 0.003 0.001 HIS K 670 PHE 0.010 0.001 PHE G 100 TYR 0.011 0.001 TYR B 48 ARG 0.005 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 735) hydrogen bonds : angle 3.39869 ( 2045) covalent geometry : bond 0.00446 (17181) covalent geometry : angle 0.55390 (24477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9149 (mttp) cc_final: 0.8778 (mttp) REVERT: A 70 GLU cc_start: 0.8894 (tp30) cc_final: 0.8457 (tp30) REVERT: A 73 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 81 ASP cc_start: 0.9043 (m-30) cc_final: 0.8768 (t0) REVERT: A 99 ASP cc_start: 0.8995 (t0) cc_final: 0.8287 (t0) REVERT: B 41 ARG cc_start: 0.9577 (ttp-170) cc_final: 0.9203 (ttp80) REVERT: B 73 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8346 (tp30) REVERT: B 99 ASP cc_start: 0.8818 (t0) cc_final: 0.8154 (t0) REVERT: B 101 GLU cc_start: 0.8457 (pm20) cc_final: 0.8067 (pm20) REVERT: C 88 ASP cc_start: 0.8965 (t0) cc_final: 0.8723 (t0) REVERT: C 96 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8320 (mm-30) REVERT: C 113 GLU cc_start: 0.8922 (mp0) cc_final: 0.8106 (mp0) REVERT: C 125 GLU cc_start: 0.8301 (tp30) cc_final: 0.8100 (tp30) REVERT: C 129 HIS cc_start: 0.9188 (OUTLIER) cc_final: 0.8834 (m-70) REVERT: D 55 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8142 (tp30) REVERT: D 57 TYR cc_start: 0.9437 (m-80) cc_final: 0.8950 (m-80) REVERT: D 88 ASP cc_start: 0.9084 (t0) cc_final: 0.8529 (t0) REVERT: D 91 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8547 (tm-30) REVERT: D 97 SER cc_start: 0.9363 (m) cc_final: 0.9053 (p) REVERT: D 125 GLU cc_start: 0.8602 (tp30) cc_final: 0.8209 (tp30) REVERT: E 50 GLU cc_start: 0.8707 (tt0) cc_final: 0.8041 (tt0) REVERT: E 115 LYS cc_start: 0.9431 (mttm) cc_final: 0.9159 (mptt) REVERT: F 50 GLU cc_start: 0.9171 (tt0) cc_final: 0.8688 (tt0) REVERT: G 53 GLU cc_start: 0.8947 (tp30) cc_final: 0.8631 (tp30) REVERT: G 59 LYS cc_start: 0.8931 (tttt) cc_final: 0.8708 (tttm) REVERT: G 100 PHE cc_start: 0.9064 (m-80) cc_final: 0.8830 (m-80) REVERT: H 27 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8933 (mm-40) REVERT: H 79 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8679 (mmtp) REVERT: K 354 MET cc_start: 0.8704 (pmm) cc_final: 0.8146 (pmm) REVERT: K 373 TRP cc_start: 0.9184 (t60) cc_final: 0.8902 (t60) REVERT: K 452 MET cc_start: 0.8019 (ttp) cc_final: 0.7754 (ttt) REVERT: K 758 MET cc_start: 0.5214 (tpt) cc_final: 0.4774 (mmm) outliers start: 19 outliers final: 16 residues processed: 198 average time/residue: 0.2918 time to fit residues: 85.1953 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 : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.086702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056349 restraints weight = 55660.545| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.82 r_work: 0.2831 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.5108 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= 0.177 Angle : 0.548 11.473 24477 Z= 0.310 Chirality : 0.034 0.151 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.368 169.224 4678 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.48 % Allowed : 18.73 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.24), residues: 1244 helix: 2.78 (0.18), residues: 810 sheet: -1.30 (0.52), residues: 78 loop : -0.46 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.006 0.001 HIS C 129 PHE 0.009 0.001 PHE G 100 TYR 0.012 0.001 TYR B 48 ARG 0.006 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 735) hydrogen bonds : angle 3.28859 ( 2045) covalent geometry : bond 0.00390 (17181) covalent geometry : angle 0.54827 (24477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9148 (mttp) cc_final: 0.8763 (mttp) REVERT: A 47 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8688 (ttp-170) REVERT: A 70 GLU cc_start: 0.8879 (tp30) cc_final: 0.8435 (tp30) REVERT: A 73 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8766 (tm-30) REVERT: A 81 ASP cc_start: 0.9026 (m-30) cc_final: 0.8673 (t0) REVERT: A 99 ASP cc_start: 0.8989 (t0) cc_final: 0.8270 (t0) REVERT: B 41 ARG cc_start: 0.9565 (ttp-170) cc_final: 0.9287 (ttp80) REVERT: B 73 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8331 (tp30) REVERT: B 99 ASP cc_start: 0.8888 (t0) cc_final: 0.7775 (t0) REVERT: C 88 ASP cc_start: 0.8953 (t0) cc_final: 0.8713 (t0) REVERT: C 96 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8304 (mm-30) REVERT: C 113 GLU cc_start: 0.8932 (mp0) cc_final: 0.8068 (mp0) REVERT: D 57 TYR cc_start: 0.9432 (m-80) cc_final: 0.8956 (m-80) REVERT: D 88 ASP cc_start: 0.9088 (t0) cc_final: 0.8530 (t0) REVERT: D 91 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 97 SER cc_start: 0.9367 (m) cc_final: 0.9040 (p) REVERT: D 125 GLU cc_start: 0.8564 (tp30) cc_final: 0.8171 (tp30) REVERT: E 50 GLU cc_start: 0.8685 (tt0) cc_final: 0.8046 (tt0) REVERT: E 115 LYS cc_start: 0.9430 (mttm) cc_final: 0.9165 (mptt) REVERT: F 50 GLU cc_start: 0.9160 (tt0) cc_final: 0.8576 (tt0) REVERT: G 53 GLU cc_start: 0.8906 (tp30) cc_final: 0.8569 (tp30) REVERT: G 59 LYS cc_start: 0.8935 (tttt) cc_final: 0.8734 (tttm) REVERT: H 79 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8709 (mmtp) REVERT: K 296 MET cc_start: 0.8708 (ppp) cc_final: 0.8492 (ppp) REVERT: K 354 MET cc_start: 0.8678 (pmm) cc_final: 0.8096 (pmm) REVERT: K 373 TRP cc_start: 0.9171 (t60) cc_final: 0.8887 (t60) REVERT: K 452 MET cc_start: 0.8014 (ttp) cc_final: 0.7725 (ttt) REVERT: K 758 MET cc_start: 0.5471 (tpt) cc_final: 0.5065 (mmm) outliers start: 16 outliers final: 15 residues processed: 197 average time/residue: 0.2702 time to fit residues: 79.1844 Evaluate side-chains 196 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.085363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053997 restraints weight = 57039.520| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.93 r_work: 0.2787 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5441 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= 0.241 Angle : 0.601 11.030 24477 Z= 0.337 Chirality : 0.036 0.150 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.659 173.887 4678 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.75 % Allowed : 19.00 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.24), residues: 1244 helix: 2.70 (0.18), residues: 813 sheet: -1.33 (0.53), residues: 78 loop : -0.45 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.006 0.001 HIS C 129 PHE 0.011 0.001 PHE G 100 TYR 0.014 0.001 TYR B 48 ARG 0.005 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 735) hydrogen bonds : angle 3.52271 ( 2045) covalent geometry : bond 0.00538 (17181) covalent geometry : angle 0.60147 (24477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9143 (mttp) cc_final: 0.8782 (mttp) REVERT: A 70 GLU cc_start: 0.8897 (tp30) cc_final: 0.8447 (tp30) REVERT: A 73 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 99 ASP cc_start: 0.9015 (t0) cc_final: 0.8299 (t0) REVERT: B 41 ARG cc_start: 0.9599 (ttp-170) cc_final: 0.9139 (ttp80) REVERT: B 73 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8362 (tp30) REVERT: B 99 ASP cc_start: 0.8530 (t0) cc_final: 0.8136 (t0) REVERT: B 101 GLU cc_start: 0.8538 (pm20) cc_final: 0.7540 (pm20) REVERT: C 88 ASP cc_start: 0.8993 (t0) cc_final: 0.8752 (t0) REVERT: C 91 GLU cc_start: 0.9264 (tp30) cc_final: 0.8925 (tp30) REVERT: C 113 GLU cc_start: 0.8906 (mp0) cc_final: 0.8059 (mp0) REVERT: D 57 TYR cc_start: 0.9449 (m-80) cc_final: 0.9076 (m-80) REVERT: D 88 ASP cc_start: 0.9101 (t0) cc_final: 0.8660 (t0) REVERT: D 91 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 97 SER cc_start: 0.9388 (m) cc_final: 0.9056 (p) REVERT: D 113 GLU cc_start: 0.8718 (mp0) cc_final: 0.8091 (mp0) REVERT: D 125 GLU cc_start: 0.8640 (tp30) cc_final: 0.8200 (tp30) REVERT: E 50 GLU cc_start: 0.8725 (tt0) cc_final: 0.8058 (tt0) REVERT: E 115 LYS cc_start: 0.9481 (mttm) cc_final: 0.9220 (mptt) REVERT: G 53 GLU cc_start: 0.8979 (tp30) cc_final: 0.8663 (tp30) REVERT: G 59 LYS cc_start: 0.8959 (tttt) cc_final: 0.8719 (tttm) REVERT: H 79 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8705 (mmtp) REVERT: H 98 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8219 (m-10) REVERT: K 296 MET cc_start: 0.8944 (ppp) cc_final: 0.8742 (ppp) REVERT: K 354 MET cc_start: 0.8736 (pmm) cc_final: 0.8151 (pmm) REVERT: K 373 TRP cc_start: 0.9178 (t60) cc_final: 0.8865 (t60) REVERT: K 452 MET cc_start: 0.7950 (ttp) cc_final: 0.7587 (ttm) REVERT: K 758 MET cc_start: 0.5479 (tpt) cc_final: 0.5078 (mmm) outliers start: 19 outliers final: 13 residues processed: 188 average time/residue: 0.2792 time to fit residues: 78.2135 Evaluate side-chains 188 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 124 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.086828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056468 restraints weight = 55764.572| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.84 r_work: 0.2852 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5414 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= 0.153 Angle : 0.555 10.652 24477 Z= 0.314 Chirality : 0.034 0.175 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.455 175.787 4678 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.11 % Allowed : 19.56 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1244 helix: 2.83 (0.18), residues: 803 sheet: -1.21 (0.52), residues: 78 loop : -0.38 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 373 HIS 0.004 0.001 HIS C 129 PHE 0.007 0.001 PHE F 67 TYR 0.011 0.001 TYR B 48 ARG 0.004 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 735) hydrogen bonds : angle 3.26380 ( 2045) covalent geometry : bond 0.00333 (17181) covalent geometry : angle 0.55484 (24477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9154 (mttp) cc_final: 0.8764 (mttp) REVERT: A 70 GLU cc_start: 0.8879 (tp30) cc_final: 0.8450 (tp30) REVERT: A 73 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 99 ASP cc_start: 0.8946 (t0) cc_final: 0.8246 (t0) REVERT: A 113 HIS cc_start: 0.9065 (m-70) cc_final: 0.8665 (m90) REVERT: B 41 ARG cc_start: 0.9487 (ttp-170) cc_final: 0.9277 (ttp80) REVERT: B 73 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8290 (tp30) REVERT: B 99 ASP cc_start: 0.8713 (t0) cc_final: 0.7918 (t0) REVERT: C 88 ASP cc_start: 0.8948 (t0) cc_final: 0.8703 (t0) REVERT: C 113 GLU cc_start: 0.8930 (mp0) cc_final: 0.8081 (mp0) REVERT: D 57 TYR cc_start: 0.9425 (m-80) cc_final: 0.8991 (m-80) REVERT: D 88 ASP cc_start: 0.9076 (t0) cc_final: 0.8513 (t0) REVERT: D 91 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 97 SER cc_start: 0.9372 (m) cc_final: 0.9069 (p) REVERT: D 113 GLU cc_start: 0.8653 (mp0) cc_final: 0.7963 (mp0) REVERT: D 125 GLU cc_start: 0.8476 (tp30) cc_final: 0.8079 (tp30) REVERT: E 50 GLU cc_start: 0.8662 (tt0) cc_final: 0.8011 (tt0) REVERT: E 115 LYS cc_start: 0.9437 (mttm) cc_final: 0.9183 (mptt) REVERT: E 133 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8113 (pt0) REVERT: F 50 GLU cc_start: 0.9107 (tt0) cc_final: 0.8761 (tt0) REVERT: G 59 LYS cc_start: 0.8880 (tttt) cc_final: 0.8676 (tttm) REVERT: G 84 MET cc_start: 0.8880 (tpp) cc_final: 0.8430 (mmm) REVERT: H 79 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8922 (mmtm) REVERT: K 354 MET cc_start: 0.8674 (pmm) cc_final: 0.8095 (pmm) REVERT: K 373 TRP cc_start: 0.9188 (t60) cc_final: 0.8904 (t60) REVERT: K 452 MET cc_start: 0.7972 (ttp) cc_final: 0.7455 (ttt) outliers start: 12 outliers final: 12 residues processed: 195 average time/residue: 0.2675 time to fit residues: 77.8644 Evaluate side-chains 198 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 50.0000 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.087666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057441 restraints weight = 55350.133| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.86 r_work: 0.2878 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5441 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= 0.145 Angle : 0.557 11.134 24477 Z= 0.312 Chirality : 0.033 0.172 2776 Planarity : 0.004 0.041 2050 Dihedral : 29.375 176.588 4678 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.11 % Allowed : 19.65 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.24), residues: 1244 helix: 2.80 (0.18), residues: 803 sheet: -1.22 (0.51), residues: 78 loop : -0.38 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 373 HIS 0.004 0.001 HIS C 129 PHE 0.008 0.001 PHE G 100 TYR 0.010 0.001 TYR B 48 ARG 0.003 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 735) hydrogen bonds : angle 3.19685 ( 2045) covalent geometry : bond 0.00316 (17181) covalent geometry : angle 0.55677 (24477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9342.51 seconds wall clock time: 161 minutes 56.00 seconds (9716.00 seconds total)