Starting phenix.real_space_refine on Fri Jul 3 19:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo2_61641/07_2026/9jo2_61641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo2_61641/07_2026/9jo2_61641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jo2_61641/07_2026/9jo2_61641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo2_61641/07_2026/9jo2_61641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jo2_61641/07_2026/9jo2_61641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo2_61641/07_2026/9jo2_61641.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 292 5.49 5 S 25 5.16 5 Cl 1 4.86 5 C 9339 2.51 5 N 2976 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16225 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4209 Classifications: {'peptide': 512} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 492} Chain breaks: 4 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.20 Number of scatterers: 16225 At special positions: 0 Unit cell: (97.425, 116.91, 156.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 25 16.00 P 292 15.00 O 3592 8.00 N 2976 7.00 C 9339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 488.2 milliseconds 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 65.6% alpha, 3.6% beta 141 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.873A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.542A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.561A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.605A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.740A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.726A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.743A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.684A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.508A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.453A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.506A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.593A pdb=" N LEU G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.588A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.672A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.534A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.520A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 114 Processing helix chain 'K' and resid 116 through 119 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 138 removed outlier: 3.786A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 137 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP K 138 " --> pdb=" O ARG K 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 130 through 138' Processing helix chain 'K' and resid 197 through 199 No H-bonds generated for 'chain 'K' and resid 197 through 199' Processing helix chain 'K' and resid 200 through 212 Processing helix chain 'K' and resid 227 through 243 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.512A pdb=" N TRP K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.831A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 329 removed outlier: 3.601A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 343 removed outlier: 3.595A pdb=" N PHE K 343 " --> pdb=" O VAL K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 371 removed outlier: 4.318A pdb=" N LEU K 363 " --> pdb=" O ASN K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 386 removed outlier: 3.557A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 406 removed outlier: 3.606A pdb=" N GLN K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR K 403 " --> pdb=" O LYS K 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU K 405 " --> pdb=" O LEU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 478 removed outlier: 3.723A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.885A pdb=" N GLN K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.825A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.216A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 4.005A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 3.554A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.136A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.942A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.065A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 298 through 302 removed outlier: 6.228A pdb=" N GLU K 319 " --> pdb=" O ASN K 347 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU K 349 " --> pdb=" O GLU K 319 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY K 217 " --> pdb=" O ARG K 348 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 428 through 431 removed outlier: 3.742A pdb=" N VAL K 627 " --> pdb=" O LEU K 429 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 1.46 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: 2996 1.33 - 1.45: 5242 1.45 - 1.57: 8251 1.57 - 1.69: 582 1.69 - 1.81: 43 Bond restraints: 17114 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.34e-02 5.57e+03 3.12e+01 bond pdb=" C3' DA J 80 " pdb=" O3' DA J 80 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.71e+01 bond pdb=" C3' DA J 90 " pdb=" O3' DA J 90 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.528 1.484 0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" C3' DA I 30 " pdb=" O3' DA I 30 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.56e+01 ... (remaining 17109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 23863 2.62 - 5.24: 463 5.24 - 7.87: 39 7.87 - 10.49: 4 10.49 - 13.11: 3 Bond angle restraints: 24372 Sorted by residual: angle pdb=" CG ARG D 30 " pdb=" CD ARG D 30 " pdb=" NE ARG D 30 " ideal model delta sigma weight residual 112.00 99.47 12.53 2.20e+00 2.07e-01 3.25e+01 angle pdb=" N VAL K 417 " pdb=" CA VAL K 417 " pdb=" C VAL K 417 " ideal model delta sigma weight residual 109.34 97.58 11.76 2.08e+00 2.31e-01 3.20e+01 angle pdb=" O4' DC I 3 " pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.19e+01 angle pdb=" C PRO K 423 " pdb=" N LYS K 424 " pdb=" CA LYS K 424 " ideal model delta sigma weight residual 121.42 113.44 7.98 1.43e+00 4.89e-01 3.11e+01 angle pdb=" O ASP K 416 " pdb=" C ASP K 416 " pdb=" N VAL K 417 " ideal model delta sigma weight residual 122.07 127.77 -5.70 1.03e+00 9.43e-01 3.06e+01 ... (remaining 24367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 8061 35.57 - 71.14: 1461 71.14 - 106.70: 34 106.70 - 142.27: 1 142.27 - 177.84: 13 Dihedral angle restraints: 9570 sinusoidal: 5836 harmonic: 3734 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 -127.22 -52.78 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA PRO K 489 " pdb=" C PRO K 489 " pdb=" N PRO K 490 " pdb=" CA PRO K 490 " ideal model delta harmonic sigma weight residual 180.00 132.26 47.74 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 148.56 31.44 0 5.00e+00 4.00e-02 3.95e+01 ... (remaining 9567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2160 0.062 - 0.125: 521 0.125 - 0.187: 78 0.187 - 0.249: 4 0.249 - 0.312: 6 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CB ILE K 244 " pdb=" CA ILE K 244 " pdb=" CG1 ILE K 244 " pdb=" CG2 ILE K 244 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA VAL K 417 " pdb=" N VAL K 417 " pdb=" C VAL K 417 " pdb=" CB VAL K 417 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' DG I 40 " pdb=" C4' DG I 40 " pdb=" O3' DG I 40 " pdb=" C2' DG I 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2766 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " -0.070 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO K 490 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 263 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" CD GLU K 263 " -0.074 2.00e-02 2.50e+03 pdb=" OE1 GLU K 263 " 0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU K 263 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN K 406 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO K 407 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO K 407 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 407 " -0.035 5.00e-02 4.00e+02 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 141 2.57 - 3.15: 13515 3.15 - 3.74: 28573 3.74 - 4.32: 39522 4.32 - 4.90: 58010 Nonbonded interactions: 139761 Sorted by model distance: nonbonded pdb=" O GLU K 535 " pdb=" OH TYR K 545 " model vdw 1.990 3.040 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.100 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.101 3.040 nonbonded pdb=" OD1 ASP K 494 " pdb=" ND1 HIS K 496 " model vdw 2.113 3.120 ... (remaining 139756 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 0.010 0.082 17114 Z= 0.743 Angle : 0.942 13.109 24372 Z= 0.725 Chirality : 0.055 0.312 2769 Planarity : 0.005 0.108 2079 Dihedral : 27.127 177.840 7150 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.10 % Favored : 90.58 % Rotamer: Outliers : 0.18 % Allowed : 0.82 % Favored : 98.99 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1253 helix: 0.65 (0.19), residues: 766 sheet: -2.24 (0.65), residues: 75 loop : -2.42 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 77 TYR 0.025 0.002 TYR K 320 PHE 0.024 0.002 PHE K 574 TRP 0.031 0.003 TRP K 267 HIS 0.008 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00994 / 0.74 (17114) covalent geometry : angle 0.94177 / 0.72 (24372) hydrogen bonds : bond 0.09812 / 6.93 ( 925) hydrogen bonds : angle 4.68746 / 3.47 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8977 (m) cc_final: 0.8767 (p) REVERT: B 59 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8438 (tttp) REVERT: B 79 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8093 (mtpm) REVERT: C 90 ASP cc_start: 0.8619 (t0) cc_final: 0.8304 (t0) REVERT: H 48 ASP cc_start: 0.8870 (p0) cc_final: 0.8230 (p0) REVERT: K 91 LEU cc_start: 0.9098 (mp) cc_final: 0.8784 (pt) REVERT: K 267 TRP cc_start: 0.8302 (m100) cc_final: 0.7568 (m100) REVERT: K 361 HIS cc_start: 0.6423 (t-90) cc_final: 0.5770 (t-170) REVERT: K 652 GLN cc_start: 0.8638 (mp10) cc_final: 0.7815 (mp10) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.6756 time to fit residues: 181.3285 Evaluate side-chains 153 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 84 GLN G 104 GLN K 111 HIS K 327 HIS ** K 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067597 restraints weight = 42363.883| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.04 r_work: 0.3068 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17114 Z= 0.203 Angle : 0.793 9.771 24372 Z= 0.434 Chirality : 0.052 0.422 2769 Planarity : 0.006 0.090 2079 Dihedral : 30.938 173.014 4599 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 1.65 % Allowed : 14.30 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1253 helix: 1.12 (0.19), residues: 765 sheet: -2.14 (0.67), residues: 71 loop : -2.21 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG D 30 TYR 0.016 0.002 TYR K 191 PHE 0.047 0.002 PHE K 109 TRP 0.016 0.002 TRP K 364 HIS 0.010 0.002 HIS K 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (17114) covalent geometry : angle 0.79296 / 0.43 (24372) hydrogen bonds : bond 0.05383 / 3.68 ( 925) hydrogen bonds : angle 3.91274 / 2.89 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8343 (tp30) REVERT: B 63 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 79 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8585 (mtpm) REVERT: D 90 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: H 48 ASP cc_start: 0.9021 (p0) cc_final: 0.8410 (p0) REVERT: K 91 LEU cc_start: 0.9189 (mp) cc_final: 0.8849 (pt) REVERT: K 223 MET cc_start: 0.8447 (tmm) cc_final: 0.8219 (tmt) REVERT: K 267 TRP cc_start: 0.8331 (m100) cc_final: 0.7927 (m100) REVERT: K 605 ASP cc_start: 0.8909 (m-30) cc_final: 0.8678 (m-30) outliers start: 18 outliers final: 9 residues processed: 193 average time/residue: 0.6652 time to fit residues: 139.5848 Evaluate side-chains 165 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 506 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS K 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.093808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067020 restraints weight = 42421.645| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17114 Z= 0.177 Angle : 0.719 10.938 24372 Z= 0.400 Chirality : 0.049 0.387 2769 Planarity : 0.005 0.090 2079 Dihedral : 30.683 169.954 4597 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.38 % Favored : 93.46 % Rotamer: Outliers : 2.84 % Allowed : 16.68 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1253 helix: 1.45 (0.19), residues: 768 sheet: -2.09 (0.67), residues: 71 loop : -2.00 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 30 TYR 0.020 0.002 TYR K 320 PHE 0.035 0.001 PHE K 109 TRP 0.018 0.002 TRP K 364 HIS 0.006 0.001 HIS K 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (17114) covalent geometry : angle 0.71937 / 0.40 (24372) hydrogen bonds : bond 0.05009 / 3.38 ( 925) hydrogen bonds : angle 3.59886 / 2.65 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7931 (mp0) REVERT: A 94 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8442 (tp30) REVERT: B 63 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8213 (mt-10) REVERT: B 79 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8601 (mtpm) REVERT: C 95 LYS cc_start: 0.9080 (tptm) cc_final: 0.8863 (tppp) REVERT: C 99 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.8086 (mmm160) REVERT: D 90 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: H 48 ASP cc_start: 0.9045 (p0) cc_final: 0.8538 (p0) REVERT: K 91 LEU cc_start: 0.9146 (mp) cc_final: 0.8809 (pt) REVERT: K 109 PHE cc_start: 0.8513 (m-80) cc_final: 0.8091 (m-80) REVERT: K 205 ASN cc_start: 0.8894 (m110) cc_final: 0.8496 (m110) REVERT: K 223 MET cc_start: 0.8454 (tmm) cc_final: 0.8173 (tmt) REVERT: K 534 LEU cc_start: 0.9322 (tt) cc_final: 0.9086 (tm) REVERT: K 605 ASP cc_start: 0.8972 (m-30) cc_final: 0.8706 (m-30) REVERT: K 609 MET cc_start: 0.8911 (mpt) cc_final: 0.8638 (mpp) outliers start: 31 outliers final: 10 residues processed: 196 average time/residue: 0.6308 time to fit residues: 134.4136 Evaluate side-chains 170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 84 GLN F 93 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS K 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.094369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067772 restraints weight = 42436.762| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.02 r_work: 0.3071 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17114 Z= 0.152 Angle : 0.684 9.488 24372 Z= 0.382 Chirality : 0.047 0.403 2769 Planarity : 0.005 0.091 2079 Dihedral : 30.565 169.949 4597 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 2.84 % Allowed : 18.88 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1253 helix: 1.55 (0.19), residues: 770 sheet: -2.13 (0.66), residues: 71 loop : -1.99 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 30 TYR 0.013 0.001 TYR K 491 PHE 0.021 0.001 PHE K 109 TRP 0.014 0.001 TRP K 364 HIS 0.006 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (17114) covalent geometry : angle 0.68412 / 0.38 (24372) hydrogen bonds : bond 0.04524 / 3.09 ( 925) hydrogen bonds : angle 3.44989 / 2.53 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8398 (tp30) REVERT: B 63 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 79 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8601 (mtpm) REVERT: C 99 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8140 (mmm160) REVERT: D 90 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: H 48 ASP cc_start: 0.9047 (p0) cc_final: 0.8561 (p0) REVERT: K 91 LEU cc_start: 0.9130 (mp) cc_final: 0.8806 (pt) REVERT: K 109 PHE cc_start: 0.8531 (m-10) cc_final: 0.8043 (m-80) REVERT: K 205 ASN cc_start: 0.8844 (m110) cc_final: 0.8487 (m110) REVERT: K 223 MET cc_start: 0.8461 (tmm) cc_final: 0.7952 (tmm) REVERT: K 266 ARG cc_start: 0.8749 (ptm-80) cc_final: 0.8219 (tmt-80) REVERT: K 493 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7822 (t) REVERT: K 605 ASP cc_start: 0.8969 (m-30) cc_final: 0.8720 (m-30) REVERT: K 609 MET cc_start: 0.8908 (mpt) cc_final: 0.8648 (mpt) REVERT: K 610 ASP cc_start: 0.8920 (t0) cc_final: 0.8264 (t0) outliers start: 31 outliers final: 13 residues processed: 195 average time/residue: 0.6199 time to fit residues: 132.0246 Evaluate side-chains 171 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 133 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN F 93 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.091887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064183 restraints weight = 42581.795| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.12 r_work: 0.2971 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17114 Z= 0.251 Angle : 0.757 9.753 24372 Z= 0.412 Chirality : 0.050 0.407 2769 Planarity : 0.005 0.116 2079 Dihedral : 30.662 170.632 4597 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 3.85 % Allowed : 19.98 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1253 helix: 1.43 (0.19), residues: 771 sheet: -2.28 (0.64), residues: 76 loop : -1.98 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 30 TYR 0.022 0.002 TYR K 545 PHE 0.015 0.002 PHE K 109 TRP 0.014 0.001 TRP K 364 HIS 0.008 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 (17114) covalent geometry : angle 0.75717 / 0.41 (24372) hydrogen bonds : bond 0.05583 / 3.76 ( 925) hydrogen bonds : angle 3.62855 / 2.67 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8029 (mp0) REVERT: A 94 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8350 (tp30) REVERT: B 63 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 79 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8713 (mtpm) REVERT: D 90 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: F 79 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8816 (ttmm) REVERT: G 73 ASN cc_start: 0.8848 (t0) cc_final: 0.8596 (t0) REVERT: H 48 ASP cc_start: 0.9116 (p0) cc_final: 0.8648 (p0) REVERT: H 110 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: K 91 LEU cc_start: 0.9158 (mp) cc_final: 0.8831 (pt) REVERT: K 109 PHE cc_start: 0.8628 (m-10) cc_final: 0.8207 (m-80) REVERT: K 201 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7379 (mp) REVERT: K 205 ASN cc_start: 0.8889 (m110) cc_final: 0.8666 (m110) REVERT: K 335 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8081 (mtm) REVERT: K 493 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7881 (t) REVERT: K 605 ASP cc_start: 0.9089 (m-30) cc_final: 0.8756 (m-30) REVERT: K 609 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8595 (mpp) outliers start: 42 outliers final: 14 residues processed: 195 average time/residue: 0.6390 time to fit residues: 135.9936 Evaluate side-chains 177 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 573 VAL Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 120 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN C 84 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.092778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065660 restraints weight = 42446.331| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.05 r_work: 0.3005 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17114 Z= 0.164 Angle : 0.699 9.611 24372 Z= 0.386 Chirality : 0.047 0.402 2769 Planarity : 0.005 0.114 2079 Dihedral : 30.509 170.223 4597 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 3.30 % Allowed : 21.08 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1253 helix: 1.59 (0.19), residues: 771 sheet: -2.21 (0.67), residues: 71 loop : -1.92 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 30 TYR 0.011 0.001 TYR K 545 PHE 0.013 0.001 PHE K 109 TRP 0.019 0.002 TRP K 364 HIS 0.006 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (17114) covalent geometry : angle 0.69868 / 0.39 (24372) hydrogen bonds : bond 0.04644 / 3.15 ( 925) hydrogen bonds : angle 3.43364 / 2.52 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.488 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: A 94 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8358 (tp30) REVERT: B 63 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 90 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: E 122 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8480 (ptmm) REVERT: F 79 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8789 (ttmm) REVERT: G 73 ASN cc_start: 0.8797 (t0) cc_final: 0.8492 (t0) REVERT: H 48 ASP cc_start: 0.9102 (p0) cc_final: 0.8628 (p0) REVERT: H 110 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: K 91 LEU cc_start: 0.9165 (mp) cc_final: 0.8838 (pt) REVERT: K 109 PHE cc_start: 0.8643 (m-10) cc_final: 0.8202 (m-80) REVERT: K 201 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7412 (mp) REVERT: K 205 ASN cc_start: 0.8850 (m110) cc_final: 0.8635 (m110) REVERT: K 223 MET cc_start: 0.8709 (tmm) cc_final: 0.8050 (tmm) REVERT: K 493 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7829 (t) REVERT: K 605 ASP cc_start: 0.9135 (m-30) cc_final: 0.8750 (m-30) REVERT: K 609 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8573 (mpp) REVERT: K 610 ASP cc_start: 0.8906 (t0) cc_final: 0.8643 (t0) outliers start: 36 outliers final: 10 residues processed: 198 average time/residue: 0.6296 time to fit residues: 136.1014 Evaluate side-chains 175 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 74 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 112 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 64 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS K 361 HIS ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.092217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064950 restraints weight = 42312.921| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.06 r_work: 0.2985 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17114 Z= 0.194 Angle : 0.717 9.952 24372 Z= 0.393 Chirality : 0.048 0.407 2769 Planarity : 0.005 0.058 2079 Dihedral : 30.469 170.193 4597 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 3.02 % Allowed : 22.36 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1253 helix: 1.55 (0.19), residues: 771 sheet: -2.15 (0.64), residues: 76 loop : -1.93 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 134 TYR 0.012 0.001 TYR K 491 PHE 0.016 0.001 PHE K 385 TRP 0.024 0.002 TRP K 364 HIS 0.007 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (17114) covalent geometry : angle 0.71686 / 0.39 (24372) hydrogen bonds : bond 0.04974 / 3.36 ( 925) hydrogen bonds : angle 3.44245 / 2.52 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8053 (mp0) REVERT: A 94 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8357 (tp30) REVERT: B 63 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8298 (mt-10) REVERT: D 90 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: E 122 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8424 (ptmm) REVERT: E 123 ASP cc_start: 0.8854 (m-30) cc_final: 0.8602 (m-30) REVERT: F 79 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8862 (ttmm) REVERT: G 73 ASN cc_start: 0.8880 (t0) cc_final: 0.8575 (t0) REVERT: H 48 ASP cc_start: 0.9123 (p0) cc_final: 0.8657 (p0) REVERT: H 110 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: K 91 LEU cc_start: 0.9157 (mp) cc_final: 0.8833 (pt) REVERT: K 109 PHE cc_start: 0.8642 (m-10) cc_final: 0.8182 (m-80) REVERT: K 201 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7485 (mp) REVERT: K 266 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8371 (tmt-80) REVERT: K 267 TRP cc_start: 0.7898 (m100) cc_final: 0.7381 (m100) REVERT: K 335 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: K 493 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7917 (t) REVERT: K 605 ASP cc_start: 0.9145 (m-30) cc_final: 0.8811 (m-30) REVERT: K 609 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8573 (mpp) outliers start: 33 outliers final: 13 residues processed: 188 average time/residue: 0.6241 time to fit residues: 127.8494 Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 38 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 88 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN K 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.092979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065546 restraints weight = 42295.205| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.06 r_work: 0.3002 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17114 Z= 0.161 Angle : 0.697 9.834 24372 Z= 0.385 Chirality : 0.046 0.405 2769 Planarity : 0.004 0.053 2079 Dihedral : 30.367 169.921 4597 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 2.57 % Allowed : 23.01 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1253 helix: 1.68 (0.19), residues: 769 sheet: -2.15 (0.68), residues: 69 loop : -1.89 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.010 0.001 TYR F 51 PHE 0.013 0.001 PHE K 109 TRP 0.026 0.002 TRP K 364 HIS 0.003 0.001 HIS K 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (17114) covalent geometry : angle 0.69712 / 0.39 (24372) hydrogen bonds : bond 0.04523 / 3.07 ( 925) hydrogen bonds : angle 3.38785 / 2.48 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8271 (mt-10) REVERT: D 90 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: E 122 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8433 (ptmm) REVERT: F 79 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8842 (ttmm) REVERT: F 80 THR cc_start: 0.9300 (m) cc_final: 0.9089 (p) REVERT: G 73 ASN cc_start: 0.8875 (t0) cc_final: 0.8549 (t0) REVERT: H 48 ASP cc_start: 0.9093 (p0) cc_final: 0.8625 (p0) REVERT: K 91 LEU cc_start: 0.9141 (mp) cc_final: 0.8827 (pt) REVERT: K 109 PHE cc_start: 0.8649 (m-10) cc_final: 0.8202 (m-80) REVERT: K 223 MET cc_start: 0.8523 (tmm) cc_final: 0.7730 (tmt) REVERT: K 229 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8989 (tm) REVERT: K 266 ARG cc_start: 0.8682 (ptm-80) cc_final: 0.8286 (tmt-80) REVERT: K 267 TRP cc_start: 0.7837 (m100) cc_final: 0.7595 (m100) REVERT: K 433 MET cc_start: 0.7854 (tpp) cc_final: 0.7087 (tmm) REVERT: K 493 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7990 (t) REVERT: K 605 ASP cc_start: 0.9132 (m-30) cc_final: 0.8795 (m-30) REVERT: K 609 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8533 (mpp) outliers start: 28 outliers final: 14 residues processed: 189 average time/residue: 0.6239 time to fit residues: 128.6920 Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 145 optimal weight: 8.9990 chunk 9 optimal weight: 0.0020 chunk 84 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 100 optimal weight: 0.0010 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.092703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065530 restraints weight = 42477.063| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.06 r_work: 0.3001 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17114 Z= 0.175 Angle : 0.714 11.173 24372 Z= 0.394 Chirality : 0.047 0.402 2769 Planarity : 0.004 0.056 2079 Dihedral : 30.337 169.852 4597 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 2.47 % Allowed : 24.01 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1253 helix: 1.69 (0.19), residues: 769 sheet: -2.18 (0.67), residues: 69 loop : -1.87 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.011 0.001 TYR K 545 PHE 0.015 0.001 PHE K 119 TRP 0.047 0.003 TRP K 384 HIS 0.012 0.001 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (17114) covalent geometry : angle 0.71444 / 0.39 (24372) hydrogen bonds : bond 0.04599 / 3.12 ( 925) hydrogen bonds : angle 3.38585 / 2.48 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8045 (mp0) REVERT: B 63 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8290 (mt-10) REVERT: D 90 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: E 122 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8426 (ptmm) REVERT: E 123 ASP cc_start: 0.8832 (m-30) cc_final: 0.8582 (m-30) REVERT: F 79 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: F 80 THR cc_start: 0.9307 (m) cc_final: 0.9096 (p) REVERT: G 73 ASN cc_start: 0.8908 (t0) cc_final: 0.8583 (t0) REVERT: H 48 ASP cc_start: 0.9101 (p0) cc_final: 0.8633 (p0) REVERT: K 91 LEU cc_start: 0.9151 (mp) cc_final: 0.8825 (pt) REVERT: K 109 PHE cc_start: 0.8648 (m-10) cc_final: 0.8161 (m-80) REVERT: K 121 HIS cc_start: 0.7983 (t70) cc_final: 0.7704 (t70) REVERT: K 223 MET cc_start: 0.8574 (tmm) cc_final: 0.7689 (tmm) REVERT: K 266 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8329 (tmt-80) REVERT: K 267 TRP cc_start: 0.7765 (m100) cc_final: 0.7332 (m100) REVERT: K 384 TRP cc_start: 0.6873 (m-10) cc_final: 0.6632 (m-10) REVERT: K 400 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: K 433 MET cc_start: 0.7778 (tpp) cc_final: 0.6970 (tmm) REVERT: K 493 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8045 (t) REVERT: K 605 ASP cc_start: 0.9136 (m-30) cc_final: 0.8771 (m-30) REVERT: K 609 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8506 (mpp) outliers start: 27 outliers final: 17 residues processed: 182 average time/residue: 0.6410 time to fit residues: 127.3917 Evaluate side-chains 183 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 496 HIS Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 108 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.093657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066647 restraints weight = 42288.047| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.04 r_work: 0.3025 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17114 Z= 0.149 Angle : 0.699 10.615 24372 Z= 0.385 Chirality : 0.047 0.485 2769 Planarity : 0.004 0.052 2079 Dihedral : 30.230 170.403 4597 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.14 % Rotamer: Outliers : 1.74 % Allowed : 24.38 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1253 helix: 1.76 (0.19), residues: 768 sheet: -2.24 (0.69), residues: 64 loop : -1.84 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.012 0.002 TYR B 88 PHE 0.013 0.001 PHE K 109 TRP 0.040 0.003 TRP K 364 HIS 0.015 0.001 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (17114) covalent geometry : angle 0.69902 / 0.39 (24372) hydrogen bonds : bond 0.04345 / 2.93 ( 925) hydrogen bonds : angle 3.35146 / 2.44 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7966 (mp0) REVERT: A 133 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7597 (mt-10) REVERT: B 63 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8300 (mt-10) REVERT: D 90 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: E 123 ASP cc_start: 0.8803 (m-30) cc_final: 0.8575 (m-30) REVERT: F 79 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8847 (ttmm) REVERT: G 73 ASN cc_start: 0.8911 (t0) cc_final: 0.8457 (t0) REVERT: H 48 ASP cc_start: 0.9090 (p0) cc_final: 0.8622 (p0) REVERT: K 91 LEU cc_start: 0.9154 (mp) cc_final: 0.8833 (pt) REVERT: K 109 PHE cc_start: 0.8657 (m-10) cc_final: 0.8199 (m-80) REVERT: K 223 MET cc_start: 0.8559 (tmm) cc_final: 0.7821 (tmt) REVERT: K 229 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8995 (tm) REVERT: K 266 ARG cc_start: 0.8707 (ptm-80) cc_final: 0.8288 (tmt-80) REVERT: K 400 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: K 433 MET cc_start: 0.7752 (tpp) cc_final: 0.6965 (tmm) REVERT: K 493 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8118 (t) REVERT: K 605 ASP cc_start: 0.9116 (m-30) cc_final: 0.8761 (m-30) REVERT: K 609 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8489 (mpp) outliers start: 19 outliers final: 11 residues processed: 185 average time/residue: 0.6278 time to fit residues: 126.6571 Evaluate side-chains 183 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.093621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066700 restraints weight = 42351.357| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.05 r_work: 0.3029 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17114 Z= 0.156 Angle : 0.710 12.607 24372 Z= 0.391 Chirality : 0.046 0.386 2769 Planarity : 0.004 0.055 2079 Dihedral : 30.201 170.515 4597 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 1.47 % Allowed : 25.94 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1253 helix: 1.76 (0.19), residues: 769 sheet: -1.64 (0.76), residues: 55 loop : -1.88 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 529 TYR 0.021 0.002 TYR D 39 PHE 0.014 0.001 PHE K 109 TRP 0.050 0.005 TRP K 267 HIS 0.008 0.001 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (17114) covalent geometry : angle 0.70991 / 0.39 (24372) hydrogen bonds : bond 0.04345 / 2.94 ( 925) hydrogen bonds : angle 3.31590 / 2.41 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4266.53 seconds wall clock time: 73 minutes 28.26 seconds (4408.26 seconds total)