Starting phenix.real_space_refine on Fri Aug 7 09:31:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2z_38023/08_2026/8x2z_38023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2z_38023/08_2026/8x2z_38023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x2z_38023/08_2026/8x2z_38023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2z_38023/08_2026/8x2z_38023.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x2z_38023/08_2026/8x2z_38023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2z_38023/08_2026/8x2z_38023.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 sd= 0.471 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5013 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 22 5.16 5 C 9831 2.51 5 N 3053 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16972 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" 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: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 699 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2364 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain: "L" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 353 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain breaks: 1 Chain: "M" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1734 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "N" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Time building chain proxies: 3.48, per 1000 atoms: 0.21 Number of scatterers: 16972 At special positions: 0 Unit cell: (133.12, 140.4, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 290 15.00 O 3776 8.00 N 3053 7.00 C 9831 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: 1.32 Conformation dependent library (CDL) restraints added in 466.6 milliseconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 49.4% alpha, 2.0% beta 141 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.604A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.014A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.621A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.900A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.710A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.866A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.752A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 49 through 62 removed outlier: 3.539A pdb=" N LEU C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 5.031A pdb=" N GLU C 66 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 80 through 87 removed outlier: 3.560A pdb=" N LEU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 87 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.144A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 60 through 87 Processing helix chain 'D' and resid 93 through 104 removed outlier: 4.222A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 removed outlier: 4.260A pdb=" N SER D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.526A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.868A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 41 removed outlier: 5.637A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.351A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 27 through 39 Processing helix chain 'G' and resid 49 through 72 removed outlier: 4.171A pdb=" N LEU G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU G 63 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 81 through 89 removed outlier: 4.325A pdb=" N LEU G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.595A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 4.077A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 3.618A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 190 removed outlier: 3.666A pdb=" N LEU K 189 " --> pdb=" O PRO K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 217 Processing helix chain 'K' and resid 246 through 254 removed outlier: 3.659A pdb=" N LEU K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 359 removed outlier: 4.753A pdb=" N LEU K 357 " --> pdb=" O TRP K 353 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR K 359 " --> pdb=" O ASP K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 377 removed outlier: 4.198A pdb=" N SER K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 391 removed outlier: 3.660A pdb=" N LEU K 391 " --> pdb=" O THR K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 416 Processing helix chain 'L' and resid 23 through 28 removed outlier: 3.950A pdb=" N ASP L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 23 through 28' Processing helix chain 'L' and resid 29 through 30 No H-bonds generated for 'chain 'L' and resid 29 through 30' Processing helix chain 'L' and resid 31 through 39 removed outlier: 4.056A pdb=" N GLU L 35 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE L 36 " --> pdb=" O GLN L 33 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR L 37 " --> pdb=" O GLN L 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP L 38 " --> pdb=" O GLU L 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 158 Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing helix chain 'M' and resid 197 through 204 removed outlier: 3.911A pdb=" N HIS M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU M 202 " --> pdb=" O HIS M 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN M 204 " --> pdb=" O ILE M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 226 removed outlier: 4.066A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS M 226 " --> pdb=" O PRO M 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 221 through 226' Processing helix chain 'M' and resid 267 through 272 Processing helix chain 'M' and resid 275 through 283 removed outlier: 3.506A pdb=" N LYS M 283 " --> pdb=" O TRP M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 286 No H-bonds generated for 'chain 'M' and resid 284 through 286' Processing helix chain 'M' and resid 354 through 359 removed outlier: 3.624A pdb=" N LEU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 11 removed outlier: 4.471A pdb=" N THR N 10 " --> pdb=" O LEU N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 24 removed outlier: 3.797A pdb=" N LEU N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 32 Processing helix chain 'N' and resid 33 through 35 No H-bonds generated for 'chain 'N' and resid 33 through 35' Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 85 through 91 removed outlier: 3.641A pdb=" N LEU N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 107 removed outlier: 3.582A pdb=" N LYS N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 111 Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.453A pdb=" N THR G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'K' and resid 170 through 172 removed outlier: 3.809A pdb=" N ILE K 170 " --> pdb=" O ILE K 177 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR K 175 " --> pdb=" O MET K 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 234 through 239 Processing sheet with id=AA7, first strand: chain 'K' and resid 288 through 289 395 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.79 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: 3343 1.33 - 1.45: 5443 1.45 - 1.57: 8478 1.57 - 1.69: 583 1.69 - 1.81: 34 Bond restraints: 17881 Sorted by residual: bond pdb=" C3' DA I 27 " pdb=" O3' DA I 27 " ideal model delta sigma weight residual 1.435 1.369 0.066 1.30e-02 5.92e+03 2.61e+01 bond pdb=" C3' DC I 89 " pdb=" O3' DC I 89 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C3' DA I 30 " pdb=" O3' DA I 30 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.82e+01 bond pdb=" C3' DG I 121 " pdb=" O3' DG I 121 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.51e+01 bond pdb=" C3' DA J 176 " pdb=" O3' DA J 176 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.49e+01 ... (remaining 17876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 24408 3.02 - 6.04: 846 6.04 - 9.06: 97 9.06 - 12.07: 22 12.07 - 15.09: 9 Bond angle restraints: 25382 Sorted by residual: angle pdb=" N VAL N 14 " pdb=" CA VAL N 14 " pdb=" C VAL N 14 " ideal model delta sigma weight residual 113.10 105.41 7.69 9.70e-01 1.06e+00 6.28e+01 angle pdb=" N ILE M 191 " pdb=" CA ILE M 191 " pdb=" C ILE M 191 " ideal model delta sigma weight residual 111.81 106.32 5.49 8.60e-01 1.35e+00 4.08e+01 angle pdb=" C ARG K 395 " pdb=" N TYR K 396 " pdb=" CA TYR K 396 " ideal model delta sigma weight residual 122.35 131.53 -9.18 1.46e+00 4.69e-01 3.95e+01 angle pdb=" N VAL M 351 " pdb=" CA VAL M 351 " pdb=" C VAL M 351 " ideal model delta sigma weight residual 113.20 107.33 5.87 9.60e-01 1.09e+00 3.74e+01 angle pdb=" O4' DA I 24 " pdb=" C1' DA I 24 " pdb=" N9 DA I 24 " ideal model delta sigma weight residual 108.00 112.25 -4.25 7.00e-01 2.04e+00 3.69e+01 ... (remaining 25377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 8412 34.59 - 69.18: 1676 69.18 - 103.77: 29 103.77 - 138.36: 1 138.36 - 172.95: 1 Dihedral angle restraints: 10119 sinusoidal: 6137 harmonic: 3982 Sorted by residual: dihedral pdb=" CA LYS K 339 " pdb=" C LYS K 339 " pdb=" N PRO K 340 " pdb=" CA PRO K 340 " ideal model delta harmonic sigma weight residual -180.00 -121.21 -58.79 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA LEU N 17 " pdb=" C LEU N 17 " pdb=" N PRO N 18 " pdb=" CA PRO N 18 " ideal model delta harmonic sigma weight residual 180.00 133.60 46.40 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" CA THR E 80 " pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta harmonic sigma weight residual -180.00 -139.18 -40.82 0 5.00e+00 4.00e-02 6.67e+01 ... (remaining 10116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2041 0.071 - 0.143: 689 0.143 - 0.214: 111 0.214 - 0.286: 21 0.286 - 0.357: 2 Chirality restraints: 2864 Sorted by residual: chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA THR C 81 " pdb=" N THR C 81 " pdb=" C THR C 81 " pdb=" CB THR C 81 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL K 268 " pdb=" CA VAL K 268 " pdb=" CG1 VAL K 268 " pdb=" CG2 VAL K 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2861 not shown) Planarity restraints: 2198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO F 32 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 339 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO K 340 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO K 340 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 340 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 17 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO N 18 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 18 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 18 " -0.041 5.00e-02 4.00e+02 ... (remaining 2195 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2273 2.75 - 3.28: 15414 3.28 - 3.82: 33655 3.82 - 4.36: 37398 4.36 - 4.90: 52263 Nonbonded interactions: 141003 Sorted by model distance: nonbonded pdb=" O THR M 223 " pdb=" OG SER M 227 " model vdw 2.207 3.040 nonbonded pdb=" O PHE L 95 " pdb=" NH1 ARG N 22 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" O THR B 80 " model vdw 2.295 3.040 nonbonded pdb=" O ALA K 351 " pdb=" OG SER K 354 " model vdw 2.297 3.040 nonbonded pdb=" O ASP M 210 " pdb=" OG SER M 213 " model vdw 2.301 3.040 ... (remaining 140998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 112) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 : 0.008 0.086 17881 Z= 0.621 Angle : 1.359 15.093 25382 Z= 0.929 Chirality : 0.071 0.357 2864 Planarity : 0.008 0.082 2198 Dihedral : 26.278 172.953 7535 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.88 % Favored : 88.89 % Rotamer: Outliers : 4.25 % Allowed : 15.01 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 1.84 % 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: -5.58 (0.16), residues: 1323 helix: -3.83 (0.13), residues: 628 sheet: -2.83 (0.80), residues: 33 loop : -3.65 (0.19), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 90 TYR 0.048 0.005 TYR N 23 PHE 0.044 0.004 PHE M 171 TRP 0.014 0.003 TRP K 353 HIS 0.013 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.62 (17881) covalent geometry : angle 1.35870 / 0.93 (25382) hydrogen bonds : bond 0.15719 / 9.55 ( 735) hydrogen bonds : angle 6.57463 / 4.65 ( 1811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 538 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.5781 (pp) cc_final: 0.5156 (pt) REVERT: A 106 ASP cc_start: 0.7028 (p0) cc_final: 0.6786 (p0) REVERT: C 67 LEU cc_start: 0.6408 (tp) cc_final: 0.6117 (tp) REVERT: D 62 MET cc_start: 0.7469 (ppp) cc_final: 0.7228 (tpt) REVERT: D 74 GLU cc_start: 0.6997 (tp30) cc_final: 0.6683 (tp30) REVERT: D 83 LEU cc_start: 0.7602 (tm) cc_final: 0.7174 (mt) REVERT: E 50 GLU cc_start: 0.7104 (tp30) cc_final: 0.6687 (tp30) REVERT: F 87 VAL cc_start: 0.7766 (m) cc_final: 0.7486 (p) REVERT: G 67 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7662 (mm) REVERT: G 87 LEU cc_start: 0.8064 (pt) cc_final: 0.7718 (pt) REVERT: H 51 THR cc_start: 0.6711 (m) cc_final: 0.6188 (p) REVERT: H 74 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7385 (tp30) REVERT: H 93 SER cc_start: 0.8660 (t) cc_final: 0.8324 (t) REVERT: H 118 THR cc_start: 0.8147 (m) cc_final: 0.7853 (p) REVERT: H 119 ARG cc_start: 0.7674 (ptm-80) cc_final: 0.7173 (ttp80) REVERT: H 122 THR cc_start: 0.8059 (m) cc_final: 0.7225 (m) REVERT: H 123 LYS cc_start: 0.8249 (mppt) cc_final: 0.7990 (mppt) REVERT: K 274 TYR cc_start: 0.7178 (m-80) cc_final: 0.6888 (m-80) REVERT: K 289 TYR cc_start: 0.5299 (p90) cc_final: 0.4899 (p90) REVERT: K 321 ILE cc_start: 0.8731 (pp) cc_final: 0.8421 (tt) REVERT: K 329 LYS cc_start: 0.7794 (ptpp) cc_final: 0.7506 (mttm) REVERT: K 333 LYS cc_start: 0.8637 (tmtm) cc_final: 0.8143 (tmtm) REVERT: K 393 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5796 (pp) REVERT: K 406 ASN cc_start: 0.6260 (m110) cc_final: 0.5583 (m-40) REVERT: L 34 GLN cc_start: 0.8393 (mm110) cc_final: 0.8176 (mp10) REVERT: M 169 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7326 (mt-10) REVERT: M 209 MET cc_start: 0.6033 (pp-130) cc_final: 0.5627 (pp-130) REVERT: M 232 PHE cc_start: 0.6551 (p90) cc_final: 0.6243 (p90) REVERT: M 238 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7601 (tm) REVERT: M 279 TRP cc_start: 0.7699 (t-100) cc_final: 0.7084 (t-100) REVERT: N 13 ASP cc_start: 0.6089 (p0) cc_final: 0.5692 (p0) REVERT: N 85 GLU cc_start: 0.8513 (pp20) cc_final: 0.8252 (pp20) outliers start: 51 outliers final: 6 residues processed: 560 average time/residue: 0.1570 time to fit residues: 122.8000 Evaluate side-chains 447 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 438 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 393 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 262 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 98 GLN E 55 GLN F 27 GLN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 GLN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 427 ASN K 440 GLN M 198 HIS M 236 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 ASN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.110863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093370 restraints weight = 53701.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095806 restraints weight = 27498.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.097438 restraints weight = 17201.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098375 restraints weight = 12395.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.099150 restraints weight = 10089.284| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17881 Z= 0.237 Angle : 1.033 14.687 25382 Z= 0.560 Chirality : 0.058 0.275 2864 Planarity : 0.008 0.130 2198 Dihedral : 29.987 173.002 4790 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.19 % Favored : 88.74 % Rotamer: Outliers : 6.84 % Allowed : 25.35 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.54 % 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: -4.51 (0.19), residues: 1323 helix: -2.64 (0.16), residues: 631 sheet: -2.08 (0.96), residues: 27 loop : -3.46 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 131 TYR 0.057 0.004 TYR D 86 PHE 0.024 0.003 PHE M 271 TRP 0.012 0.002 TRP K 247 HIS 0.008 0.002 HIS M 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.24 (17881) covalent geometry : angle 1.03275 / 0.56 (25382) hydrogen bonds : bond 0.07228 / 4.65 ( 735) hydrogen bonds : angle 4.99418 / 3.41 ( 1811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 467 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7262 (mtm110) cc_final: 0.6959 (mtm110) REVERT: A 59 GLU cc_start: 0.7820 (pp20) cc_final: 0.7257 (pp20) REVERT: A 63 ARG cc_start: 0.7680 (mtt90) cc_final: 0.7156 (mtt90) REVERT: A 105 GLU cc_start: 0.7758 (pp20) cc_final: 0.7348 (pp20) REVERT: B 34 ILE cc_start: 0.8397 (pp) cc_final: 0.8120 (pp) REVERT: B 55 ARG cc_start: 0.8368 (mpp80) cc_final: 0.8004 (mtm-85) REVERT: C 37 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8236 (ttt-90) REVERT: C 63 GLU cc_start: 0.6424 (pm20) cc_final: 0.6107 (pm20) REVERT: D 74 GLU cc_start: 0.6974 (tp30) cc_final: 0.6647 (tp30) REVERT: D 86 TYR cc_start: 0.7529 (p90) cc_final: 0.7219 (p90) REVERT: E 42 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6108 (pmmt) REVERT: F 36 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6433 (mtt90) REVERT: F 72 TYR cc_start: 0.8323 (m-80) cc_final: 0.8097 (m-80) REVERT: F 79 LYS cc_start: 0.7675 (ptmm) cc_final: 0.6963 (tppt) REVERT: F 87 VAL cc_start: 0.7838 (m) cc_final: 0.7542 (p) REVERT: F 98 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7201 (t80) REVERT: G 24 LEU cc_start: 0.8016 (mm) cc_final: 0.7691 (mp) REVERT: G 67 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7635 (mm) REVERT: H 116 GLU cc_start: 0.6585 (pp20) cc_final: 0.6334 (pp20) REVERT: H 119 ARG cc_start: 0.7791 (ptm-80) cc_final: 0.7466 (ttt-90) REVERT: K 172 MET cc_start: 0.6526 (tmm) cc_final: 0.6039 (tmm) REVERT: K 210 GLN cc_start: 0.5812 (OUTLIER) cc_final: 0.5562 (pp30) REVERT: K 249 ARG cc_start: 0.2768 (ttt180) cc_final: 0.2176 (ttp80) REVERT: K 333 LYS cc_start: 0.8539 (tmtm) cc_final: 0.8151 (tmtm) REVERT: K 350 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.6902 (mmm-85) REVERT: K 376 MET cc_start: 0.7774 (mmm) cc_final: 0.7557 (mmm) REVERT: K 379 MET cc_start: 0.5146 (tmt) cc_final: 0.4504 (tmt) REVERT: K 393 ILE cc_start: 0.5472 (OUTLIER) cc_final: 0.5269 (pp) REVERT: L 34 GLN cc_start: 0.8299 (mm110) cc_final: 0.8060 (mm-40) REVERT: M 133 TYR cc_start: 0.4876 (m-80) cc_final: 0.3863 (m-80) REVERT: M 197 GLU cc_start: 0.7786 (mp0) cc_final: 0.6309 (mp0) REVERT: M 209 MET cc_start: 0.5381 (pp-130) cc_final: 0.5067 (pp-130) REVERT: M 232 PHE cc_start: 0.6713 (p90) cc_final: 0.6304 (p90) REVERT: N 23 TYR cc_start: 0.5969 (m-80) cc_final: 0.5716 (m-80) REVERT: N 25 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6096 (tp) REVERT: N 85 GLU cc_start: 0.8607 (pp20) cc_final: 0.8240 (pp20) outliers start: 82 outliers final: 41 residues processed: 505 average time/residue: 0.1567 time to fit residues: 109.7509 Evaluate side-chains 481 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 433 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 393 ILE Chi-restraints excluded: chain M residue 141 PHE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 147 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 74 optimal weight: 0.0870 chunk 101 optimal weight: 6.9990 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 84 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 98 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN H 52 HIS H 59 GLN H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 GLN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 ASN M 258 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.109926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092312 restraints weight = 54837.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094676 restraints weight = 28450.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096249 restraints weight = 17970.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097264 restraints weight = 13150.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097850 restraints weight = 10700.623| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17881 Z= 0.227 Angle : 0.986 19.021 25382 Z= 0.535 Chirality : 0.055 0.257 2864 Planarity : 0.007 0.104 2198 Dihedral : 29.807 171.032 4781 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 8.17 % Allowed : 26.36 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.23 % 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: -4.04 (0.19), residues: 1323 helix: -2.14 (0.17), residues: 628 sheet: -2.06 (0.96), residues: 27 loop : -3.32 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 90 TYR 0.034 0.003 TYR D 86 PHE 0.032 0.003 PHE M 217 TRP 0.046 0.004 TRP M 279 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (17881) covalent geometry : angle 0.98570 / 0.53 (25382) hydrogen bonds : bond 0.06764 / 4.40 ( 735) hydrogen bonds : angle 4.69315 / 3.19 ( 1811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 464 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 59 GLU cc_start: 0.8083 (pp20) cc_final: 0.7575 (pp20) REVERT: A 60 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6380 (tp) REVERT: A 63 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7430 (mtt90) REVERT: A 105 GLU cc_start: 0.7789 (pp20) cc_final: 0.7453 (pp20) REVERT: A 131 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8607 (mtp85) REVERT: B 31 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7873 (ttpp) REVERT: B 34 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8268 (pp) REVERT: D 46 LYS cc_start: 0.7436 (pptt) cc_final: 0.7157 (pptt) REVERT: D 74 GLU cc_start: 0.7144 (tp30) cc_final: 0.6765 (tp30) REVERT: D 82 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8020 (mtpp) REVERT: D 86 TYR cc_start: 0.7792 (p90) cc_final: 0.7296 (p90) REVERT: E 62 ILE cc_start: 0.8471 (tp) cc_final: 0.8023 (tt) REVERT: E 73 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6573 (mt-10) REVERT: E 94 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: F 60 SER cc_start: 0.8015 (m) cc_final: 0.7708 (t) REVERT: F 79 LYS cc_start: 0.7747 (ptmm) cc_final: 0.7191 (tppt) REVERT: F 87 VAL cc_start: 0.8065 (m) cc_final: 0.7829 (p) REVERT: G 21 ARG cc_start: 0.8094 (ptt90) cc_final: 0.7756 (ppt170) REVERT: G 24 LEU cc_start: 0.8032 (mm) cc_final: 0.7760 (mp) REVERT: G 67 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7770 (mm) REVERT: G 102 THR cc_start: 0.7923 (p) cc_final: 0.7625 (p) REVERT: H 70 ASN cc_start: 0.8574 (t0) cc_final: 0.8336 (t0) REVERT: H 96 GLU cc_start: 0.8159 (pm20) cc_final: 0.7798 (pm20) REVERT: K 172 MET cc_start: 0.6522 (tmm) cc_final: 0.6229 (tmm) REVERT: K 243 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8052 (pmtt) REVERT: K 323 PHE cc_start: 0.7496 (t80) cc_final: 0.6980 (t80) REVERT: K 333 LYS cc_start: 0.8696 (tmtm) cc_final: 0.8278 (tmtm) REVERT: K 406 ASN cc_start: 0.7032 (m110) cc_final: 0.6547 (m110) REVERT: L 34 GLN cc_start: 0.8363 (mm110) cc_final: 0.8113 (mm-40) REVERT: M 197 GLU cc_start: 0.7575 (mp0) cc_final: 0.7042 (mm-30) REVERT: M 209 MET cc_start: 0.5397 (pp-130) cc_final: 0.5106 (pp-130) REVERT: M 232 PHE cc_start: 0.6673 (p90) cc_final: 0.6331 (p90) REVERT: M 345 LYS cc_start: 0.7384 (mmtp) cc_final: 0.7044 (mmtt) REVERT: N 85 GLU cc_start: 0.8643 (pp20) cc_final: 0.8268 (pp20) outliers start: 98 outliers final: 56 residues processed: 504 average time/residue: 0.1526 time to fit residues: 106.6300 Evaluate side-chains 498 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 437 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain M residue 141 PHE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 0.4980 chunk 54 optimal weight: 0.0370 chunk 95 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 130 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN B 25 ASN D 98 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 HIS ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.111556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093950 restraints weight = 54864.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096365 restraints weight = 28764.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097945 restraints weight = 18307.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098952 restraints weight = 13457.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.099600 restraints weight = 11005.009| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17881 Z= 0.183 Angle : 0.932 17.082 25382 Z= 0.501 Chirality : 0.052 0.322 2864 Planarity : 0.007 0.138 2198 Dihedral : 29.677 169.635 4777 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 6.84 % Allowed : 28.36 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.31 % 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: -3.68 (0.20), residues: 1323 helix: -1.83 (0.19), residues: 625 sheet: -1.97 (0.92), residues: 27 loop : -3.15 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 278 TYR 0.034 0.003 TYR N 23 PHE 0.020 0.002 PHE E 67 TRP 0.040 0.002 TRP M 279 HIS 0.004 0.001 HIS K 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (17881) covalent geometry : angle 0.93159 / 0.50 (25382) hydrogen bonds : bond 0.05976 / 3.89 ( 735) hydrogen bonds : angle 4.49317 / 3.06 ( 1811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 446 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7316 (tpp80) cc_final: 0.6982 (mmm160) REVERT: A 50 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 59 GLU cc_start: 0.7943 (pp20) cc_final: 0.7500 (pp20) REVERT: A 60 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6204 (tp) REVERT: A 97 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7121 (tt0) REVERT: A 105 GLU cc_start: 0.7829 (pp20) cc_final: 0.7441 (pp20) REVERT: A 131 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8572 (mtp85) REVERT: B 31 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7946 (ttpp) REVERT: B 55 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8102 (mtt-85) REVERT: C 21 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5323 (ppp-140) REVERT: C 70 ASN cc_start: 0.4280 (t0) cc_final: 0.3893 (t0) REVERT: C 79 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7654 (ttp80) REVERT: D 74 GLU cc_start: 0.7153 (tp30) cc_final: 0.6689 (tp30) REVERT: D 82 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8030 (mtpp) REVERT: D 86 TYR cc_start: 0.7697 (p90) cc_final: 0.7059 (p90) REVERT: E 94 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: F 52 GLU cc_start: 0.7285 (pm20) cc_final: 0.6835 (pm20) REVERT: F 60 SER cc_start: 0.8015 (m) cc_final: 0.7783 (t) REVERT: F 79 LYS cc_start: 0.7632 (ptmm) cc_final: 0.7022 (tppt) REVERT: F 87 VAL cc_start: 0.8114 (m) cc_final: 0.7868 (p) REVERT: G 21 ARG cc_start: 0.7973 (ptt90) cc_final: 0.7690 (ppt170) REVERT: G 67 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7587 (mm) REVERT: H 49 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7390 (tmmt) REVERT: H 70 ASN cc_start: 0.8545 (t0) cc_final: 0.8328 (t0) REVERT: H 96 GLU cc_start: 0.8155 (pm20) cc_final: 0.7880 (pm20) REVERT: K 172 MET cc_start: 0.6570 (tmm) cc_final: 0.6330 (tmm) REVERT: K 249 ARG cc_start: 0.3282 (ttt-90) cc_final: 0.2585 (ttp80) REVERT: K 333 LYS cc_start: 0.8706 (tmtm) cc_final: 0.8340 (tmtm) REVERT: M 149 LYS cc_start: 0.5875 (ptmt) cc_final: 0.5634 (pttt) REVERT: M 155 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7717 (mm-30) REVERT: M 209 MET cc_start: 0.5294 (pp-130) cc_final: 0.5024 (pp-130) REVERT: M 232 PHE cc_start: 0.6712 (p90) cc_final: 0.5776 (p90) REVERT: N 85 GLU cc_start: 0.8677 (pp20) cc_final: 0.8168 (pp20) outliers start: 82 outliers final: 44 residues processed: 479 average time/residue: 0.1683 time to fit residues: 111.3275 Evaluate side-chains 484 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain M residue 141 PHE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 22 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 81 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN D 98 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 386 HIS K 401 HIS M 243 ASN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.111511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094134 restraints weight = 53679.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096454 restraints weight = 28954.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097965 restraints weight = 18750.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098939 restraints weight = 13930.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099565 restraints weight = 11471.771| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17881 Z= 0.179 Angle : 0.918 17.518 25382 Z= 0.493 Chirality : 0.051 0.249 2864 Planarity : 0.007 0.097 2198 Dihedral : 29.588 169.347 4777 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 7.76 % Allowed : 29.52 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.31 % 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: -3.60 (0.20), residues: 1323 helix: -1.70 (0.19), residues: 624 sheet: -1.77 (0.94), residues: 22 loop : -3.19 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 44 TYR 0.028 0.002 TYR D 86 PHE 0.038 0.002 PHE M 217 TRP 0.040 0.002 TRP M 279 HIS 0.014 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (17881) covalent geometry : angle 0.91836 / 0.49 (25382) hydrogen bonds : bond 0.05925 / 3.88 ( 735) hydrogen bonds : angle 4.43586 / 3.01 ( 1811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 447 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 59 GLU cc_start: 0.8037 (pp20) cc_final: 0.7744 (pp20) REVERT: A 60 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6024 (tp) REVERT: A 97 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6924 (tt0) REVERT: A 106 ASP cc_start: 0.7381 (p0) cc_final: 0.7156 (p0) REVERT: A 120 GLN cc_start: 0.6969 (mp10) cc_final: 0.6530 (mt0) REVERT: C 21 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5410 (ppp-140) REVERT: D 64 ILE cc_start: 0.7440 (mm) cc_final: 0.7213 (mm) REVERT: D 74 GLU cc_start: 0.7195 (tp30) cc_final: 0.6699 (tp30) REVERT: E 42 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6256 (pmmt) REVERT: E 81 ASP cc_start: 0.8306 (p0) cc_final: 0.8089 (p0) REVERT: E 83 ARG cc_start: 0.7178 (mmp80) cc_final: 0.6947 (mmp80) REVERT: E 121 LYS cc_start: 0.8296 (mttp) cc_final: 0.8053 (mptt) REVERT: F 60 SER cc_start: 0.7972 (m) cc_final: 0.7761 (t) REVERT: F 74 GLU cc_start: 0.7453 (pp20) cc_final: 0.7175 (pp20) REVERT: G 21 ARG cc_start: 0.7972 (ptt90) cc_final: 0.7675 (ppt170) REVERT: G 44 ARG cc_start: 0.6847 (tmm160) cc_final: 0.6635 (tmm160) REVERT: G 67 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7762 (mm) REVERT: H 46 LYS cc_start: 0.8242 (tttm) cc_final: 0.7836 (tttm) REVERT: H 49 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7350 (tmmt) REVERT: H 96 GLU cc_start: 0.8094 (pm20) cc_final: 0.7754 (pm20) REVERT: K 249 ARG cc_start: 0.3449 (ttt-90) cc_final: 0.2636 (ttp80) REVERT: K 301 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7282 (p0) REVERT: K 321 ILE cc_start: 0.8609 (tt) cc_final: 0.8339 (tp) REVERT: K 322 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: K 329 LYS cc_start: 0.7846 (mttm) cc_final: 0.7575 (mttp) REVERT: K 333 LYS cc_start: 0.8756 (tmtm) cc_final: 0.8407 (tmtm) REVERT: K 373 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8499 (mp) REVERT: K 374 SER cc_start: 0.8278 (m) cc_final: 0.7936 (p) REVERT: M 149 LYS cc_start: 0.5976 (ptmt) cc_final: 0.5649 (pttt) REVERT: M 167 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.4502 (pmt-80) REVERT: M 209 MET cc_start: 0.5464 (pp-130) cc_final: 0.5133 (pp-130) REVERT: M 279 TRP cc_start: 0.7127 (t-100) cc_final: 0.6771 (t-100) REVERT: M 290 GLU cc_start: -0.1370 (OUTLIER) cc_final: -0.1832 (pt0) REVERT: N 85 GLU cc_start: 0.8693 (pp20) cc_final: 0.8053 (pp20) REVERT: N 86 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7532 (mmmt) outliers start: 93 outliers final: 50 residues processed: 488 average time/residue: 0.1686 time to fit residues: 113.3591 Evaluate side-chains 490 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 430 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 301 ASN Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 290 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 131 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 136 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 93 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 27 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 386 HIS ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.109144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.091854 restraints weight = 53581.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094062 restraints weight = 29185.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095537 restraints weight = 19091.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096474 restraints weight = 14257.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.097065 restraints weight = 11781.895| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 17881 Z= 0.229 Angle : 0.966 15.989 25382 Z= 0.518 Chirality : 0.054 0.377 2864 Planarity : 0.007 0.093 2198 Dihedral : 29.549 168.613 4777 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.02 % Favored : 87.91 % Rotamer: Outliers : 7.42 % Allowed : 31.86 % Favored : 60.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.23 % 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: -3.66 (0.20), residues: 1323 helix: -1.68 (0.18), residues: 641 sheet: -1.86 (0.99), residues: 27 loop : -3.31 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 313 TYR 0.072 0.003 TYR K 352 PHE 0.038 0.003 PHE M 217 TRP 0.021 0.002 TRP M 279 HIS 0.006 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (17881) covalent geometry : angle 0.96570 / 0.52 (25382) hydrogen bonds : bond 0.06701 / 4.35 ( 735) hydrogen bonds : angle 4.52851 / 3.12 ( 1811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 448 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7381 (tpp80) cc_final: 0.6927 (mmm160) REVERT: A 49 ARG cc_start: 0.8558 (mtp85) cc_final: 0.8284 (mtp-110) REVERT: A 50 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 76 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: A 77 ASP cc_start: 0.8400 (p0) cc_final: 0.7916 (p0) REVERT: A 105 GLU cc_start: 0.7957 (pp20) cc_final: 0.7631 (pp20) REVERT: A 120 GLN cc_start: 0.7544 (mp10) cc_final: 0.7292 (mt0) REVERT: C 21 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6689 (ppp-140) REVERT: D 62 MET cc_start: 0.8099 (mmm) cc_final: 0.7770 (mmm) REVERT: D 64 ILE cc_start: 0.7773 (mm) cc_final: 0.7560 (mm) REVERT: D 74 GLU cc_start: 0.7358 (tp30) cc_final: 0.6784 (tp30) REVERT: D 79 GLU cc_start: 0.7445 (pp20) cc_final: 0.7167 (pp20) REVERT: D 82 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8219 (mmmt) REVERT: D 88 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8705 (tppt) REVERT: F 51 TYR cc_start: 0.8375 (m-10) cc_final: 0.8105 (m-80) REVERT: F 53 GLU cc_start: 0.7351 (pm20) cc_final: 0.6940 (pm20) REVERT: F 60 SER cc_start: 0.7917 (m) cc_final: 0.7686 (t) REVERT: F 74 GLU cc_start: 0.7484 (pp20) cc_final: 0.7210 (pp20) REVERT: G 21 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7703 (ppt170) REVERT: G 38 HIS cc_start: 0.7233 (t70) cc_final: 0.6752 (t70) REVERT: G 52 TYR cc_start: 0.6833 (t80) cc_final: 0.6579 (t80) REVERT: G 59 TYR cc_start: 0.6632 (p90) cc_final: 0.6369 (p90) REVERT: H 46 LYS cc_start: 0.8337 (tttm) cc_final: 0.8122 (tttm) REVERT: H 48 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8056 (pp) REVERT: H 96 GLU cc_start: 0.7976 (pm20) cc_final: 0.7407 (pm20) REVERT: K 233 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.3252 (p90) REVERT: K 316 TYR cc_start: 0.4132 (m-10) cc_final: 0.3900 (m-10) REVERT: K 321 ILE cc_start: 0.8697 (tt) cc_final: 0.8426 (tp) REVERT: K 329 LYS cc_start: 0.7898 (mttm) cc_final: 0.7494 (mtpp) REVERT: K 373 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8513 (mp) REVERT: M 149 LYS cc_start: 0.6345 (ptmt) cc_final: 0.5985 (pttt) REVERT: M 167 ARG cc_start: 0.5727 (OUTLIER) cc_final: 0.4519 (pmt-80) REVERT: M 168 ASP cc_start: 0.7211 (p0) cc_final: 0.6985 (p0) REVERT: M 209 MET cc_start: 0.5465 (pp-130) cc_final: 0.5145 (pp-130) REVERT: M 285 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: N 85 GLU cc_start: 0.8684 (pp20) cc_final: 0.8294 (pp20) outliers start: 89 outliers final: 51 residues processed: 485 average time/residue: 0.1498 time to fit residues: 99.9492 Evaluate side-chains 490 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 432 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain K residue 229 TYR Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 301 ASN Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 285 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 294 GLN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 HIS N 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093518 restraints weight = 54336.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.095784 restraints weight = 29307.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097293 restraints weight = 19084.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098246 restraints weight = 14261.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098858 restraints weight = 11850.461| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17881 Z= 0.181 Angle : 0.935 16.197 25382 Z= 0.495 Chirality : 0.052 0.301 2864 Planarity : 0.007 0.115 2198 Dihedral : 29.499 168.708 4773 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 6.51 % Allowed : 33.86 % Favored : 59.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.31 % 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: -3.56 (0.20), residues: 1323 helix: -1.62 (0.18), residues: 639 sheet: -1.62 (1.03), residues: 27 loop : -3.24 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 35 TYR 0.032 0.002 TYR D 86 PHE 0.038 0.002 PHE M 217 TRP 0.012 0.002 TRP K 247 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (17881) covalent geometry : angle 0.93451 / 0.50 (25382) hydrogen bonds : bond 0.05933 / 3.94 ( 735) hydrogen bonds : angle 4.39401 / 3.00 ( 1811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 439 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8229 (mtp-110) REVERT: A 50 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 76 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: A 77 ASP cc_start: 0.8368 (p0) cc_final: 0.7930 (p0) REVERT: A 94 GLU cc_start: 0.7690 (tp30) cc_final: 0.7358 (tp30) REVERT: A 97 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6992 (tt0) REVERT: A 105 GLU cc_start: 0.7933 (pp20) cc_final: 0.7711 (pp20) REVERT: D 62 MET cc_start: 0.8097 (mmm) cc_final: 0.7868 (mmm) REVERT: D 74 GLU cc_start: 0.7346 (tp30) cc_final: 0.6754 (tp30) REVERT: D 79 GLU cc_start: 0.7437 (pp20) cc_final: 0.7184 (pp20) REVERT: D 82 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8255 (mmmt) REVERT: F 50 ILE cc_start: 0.8229 (pt) cc_final: 0.7900 (mm) REVERT: F 51 TYR cc_start: 0.8443 (m-10) cc_final: 0.8225 (m-80) REVERT: F 92 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8508 (tmt-80) REVERT: G 21 ARG cc_start: 0.8030 (ptt90) cc_final: 0.7690 (ppt170) REVERT: G 44 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7119 (ttp80) REVERT: G 52 TYR cc_start: 0.6712 (t80) cc_final: 0.6449 (t80) REVERT: H 38 GLU cc_start: 0.7267 (pp20) cc_final: 0.6837 (pp20) REVERT: H 96 GLU cc_start: 0.8067 (pm20) cc_final: 0.7450 (pm20) REVERT: H 108 GLU cc_start: 0.7536 (mp0) cc_final: 0.7303 (mp0) REVERT: K 233 TYR cc_start: 0.4993 (OUTLIER) cc_final: 0.3146 (p90) REVERT: K 322 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: K 329 LYS cc_start: 0.7857 (mttm) cc_final: 0.7463 (mttp) REVERT: K 352 TYR cc_start: 0.8089 (t80) cc_final: 0.7768 (t80) REVERT: M 149 LYS cc_start: 0.6370 (ptmt) cc_final: 0.5961 (pttt) REVERT: M 209 MET cc_start: 0.5472 (pp-130) cc_final: 0.5180 (pp-130) REVERT: M 285 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: N 85 GLU cc_start: 0.8737 (pp20) cc_final: 0.8491 (pp20) REVERT: N 94 LEU cc_start: 0.7691 (tp) cc_final: 0.7428 (pp) outliers start: 78 outliers final: 48 residues processed: 476 average time/residue: 0.1668 time to fit residues: 109.9859 Evaluate side-chains 481 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 428 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 285 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 135 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 ASN M 239 ASN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.111767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094011 restraints weight = 54808.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096297 restraints weight = 29689.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097804 restraints weight = 19408.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.098770 restraints weight = 14535.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.099386 restraints weight = 12045.306| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17881 Z= 0.181 Angle : 0.942 15.702 25382 Z= 0.497 Chirality : 0.052 0.282 2864 Planarity : 0.007 0.115 2198 Dihedral : 29.468 169.801 4773 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 5.92 % Allowed : 34.61 % Favored : 59.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.23 % 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: -3.49 (0.21), residues: 1323 helix: -1.55 (0.19), residues: 638 sheet: -1.52 (1.06), residues: 27 loop : -3.22 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 79 TYR 0.041 0.002 TYR N 23 PHE 0.038 0.002 PHE M 217 TRP 0.013 0.001 TRP M 279 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (17881) covalent geometry : angle 0.94213 / 0.50 (25382) hydrogen bonds : bond 0.05792 / 3.84 ( 735) hydrogen bonds : angle 4.44773 / 3.05 ( 1811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 438 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8266 (mtp-110) REVERT: A 50 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 76 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: A 77 ASP cc_start: 0.8331 (p0) cc_final: 0.7893 (p0) REVERT: A 105 GLU cc_start: 0.7902 (pp20) cc_final: 0.7627 (pp20) REVERT: A 123 ASP cc_start: 0.7538 (m-30) cc_final: 0.7231 (m-30) REVERT: B 92 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6445 (tpt-90) REVERT: D 62 MET cc_start: 0.8131 (mmm) cc_final: 0.7891 (mmm) REVERT: D 79 GLU cc_start: 0.7454 (pp20) cc_final: 0.7077 (pp20) REVERT: D 82 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8198 (mmmt) REVERT: F 35 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: F 84 LEU cc_start: 0.8068 (tp) cc_final: 0.7803 (tt) REVERT: F 92 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8433 (tmt-80) REVERT: G 21 ARG cc_start: 0.8015 (ptt90) cc_final: 0.7684 (ppt170) REVERT: G 44 ARG cc_start: 0.7486 (ttp80) cc_final: 0.7135 (ttp80) REVERT: H 38 GLU cc_start: 0.7167 (pp20) cc_final: 0.6741 (pp20) REVERT: H 96 GLU cc_start: 0.8057 (pm20) cc_final: 0.7502 (pm20) REVERT: K 233 TYR cc_start: 0.5081 (OUTLIER) cc_final: 0.3576 (p90) REVERT: K 242 ARG cc_start: 0.8153 (tpt-90) cc_final: 0.7857 (ttt90) REVERT: K 252 CYS cc_start: 0.8121 (p) cc_final: 0.7537 (t) REVERT: K 316 TYR cc_start: 0.4358 (m-10) cc_final: 0.4017 (m-10) REVERT: K 329 LYS cc_start: 0.7836 (mttm) cc_final: 0.7406 (mttp) REVERT: K 349 TYR cc_start: 0.5638 (p90) cc_final: 0.4480 (p90) REVERT: K 374 SER cc_start: 0.8400 (m) cc_final: 0.8110 (p) REVERT: M 149 LYS cc_start: 0.6371 (ptmt) cc_final: 0.5905 (pttt) REVERT: M 164 MET cc_start: 0.4345 (mmm) cc_final: 0.3993 (mmp) REVERT: M 209 MET cc_start: 0.5424 (pp-130) cc_final: 0.5133 (pp-130) REVERT: M 215 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8259 (pp) REVERT: M 285 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6272 (mp0) outliers start: 71 outliers final: 48 residues processed: 471 average time/residue: 0.1680 time to fit residues: 108.5448 Evaluate side-chains 476 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 422 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 285 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 123 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN G 38 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS M 163 ASN M 239 ASN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.111933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094297 restraints weight = 54620.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096520 restraints weight = 30483.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098003 restraints weight = 20240.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098965 restraints weight = 15257.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099583 restraints weight = 12664.870| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17881 Z= 0.185 Angle : 0.964 16.443 25382 Z= 0.503 Chirality : 0.052 0.270 2864 Planarity : 0.007 0.105 2198 Dihedral : 29.413 171.041 4771 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 6.09 % Allowed : 35.20 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.15 % 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: -3.47 (0.21), residues: 1323 helix: -1.61 (0.18), residues: 630 sheet: -1.80 (1.03), residues: 27 loop : -3.09 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 235 TYR 0.032 0.002 TYR G 52 PHE 0.046 0.002 PHE M 217 TRP 0.017 0.002 TRP K 247 HIS 0.005 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (17881) covalent geometry : angle 0.96401 / 0.50 (25382) hydrogen bonds : bond 0.05767 / 3.81 ( 735) hydrogen bonds : angle 4.50177 / 3.10 ( 1811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 437 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8242 (mtp-110) REVERT: A 50 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 76 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: A 77 ASP cc_start: 0.8306 (p0) cc_final: 0.7873 (p0) REVERT: A 129 ARG cc_start: 0.8001 (tmt-80) cc_final: 0.7795 (tmt-80) REVERT: B 92 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.6442 (tpt-90) REVERT: D 60 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8707 (mtpp) REVERT: D 62 MET cc_start: 0.8114 (mmm) cc_final: 0.7913 (mmm) REVERT: D 79 GLU cc_start: 0.7408 (pp20) cc_final: 0.7012 (pp20) REVERT: D 82 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8251 (mmmt) REVERT: D 102 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8201 (ttp80) REVERT: E 83 ARG cc_start: 0.7345 (mmp80) cc_final: 0.6954 (mmp80) REVERT: F 44 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8437 (mtpp) REVERT: F 92 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8509 (tmt-80) REVERT: G 21 ARG cc_start: 0.8042 (ptt90) cc_final: 0.7690 (ppt170) REVERT: G 44 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7181 (ttp80) REVERT: H 96 GLU cc_start: 0.8043 (pm20) cc_final: 0.7483 (pm20) REVERT: K 217 LYS cc_start: 0.7738 (pttp) cc_final: 0.7491 (ptpp) REVERT: K 233 TYR cc_start: 0.5157 (OUTLIER) cc_final: 0.3376 (p90) REVERT: K 252 CYS cc_start: 0.8192 (p) cc_final: 0.7488 (t) REVERT: K 276 MET cc_start: 0.7350 (tpp) cc_final: 0.7050 (tpp) REVERT: K 316 TYR cc_start: 0.4365 (m-10) cc_final: 0.4056 (m-10) REVERT: K 374 SER cc_start: 0.8435 (m) cc_final: 0.8107 (p) REVERT: M 149 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5912 (pttp) REVERT: M 155 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7946 (mm-30) REVERT: M 157 CYS cc_start: 0.7424 (p) cc_final: 0.6829 (p) REVERT: M 209 MET cc_start: 0.5423 (pp-130) cc_final: 0.5136 (pp-130) REVERT: M 215 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8238 (pp) REVERT: M 221 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6806 (mmtt) REVERT: M 232 PHE cc_start: 0.7030 (p90) cc_final: 0.6800 (p90) REVERT: M 237 GLN cc_start: 0.6664 (pm20) cc_final: 0.6209 (pm20) REVERT: M 285 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6120 (mp0) REVERT: M 349 LEU cc_start: 0.5794 (mt) cc_final: 0.5447 (mt) REVERT: N 25 LEU cc_start: 0.5884 (mt) cc_final: 0.5628 (mm) outliers start: 73 outliers final: 48 residues processed: 472 average time/residue: 0.1834 time to fit residues: 118.4725 Evaluate side-chains 477 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 422 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 285 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 59 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 42 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 0.0170 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS D 50 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 363 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093991 restraints weight = 54766.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096209 restraints weight = 30294.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097690 restraints weight = 19934.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.098672 restraints weight = 14993.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099297 restraints weight = 12443.456| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.341 17881 Z= 0.258 Angle : 1.087 59.200 25382 Z= 0.594 Chirality : 0.056 0.784 2864 Planarity : 0.008 0.161 2198 Dihedral : 29.415 171.065 4771 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 5.34 % Allowed : 36.28 % Favored : 58.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.15 % 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: -3.47 (0.21), residues: 1323 helix: -1.62 (0.18), residues: 630 sheet: -1.82 (1.02), residues: 27 loop : -3.08 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.002 ARG B 45 TYR 0.032 0.003 TYR K 352 PHE 0.042 0.002 PHE M 217 TRP 0.014 0.002 TRP M 279 HIS 0.003 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.26 (17881) covalent geometry : angle 1.08739 / 0.59 (25382) hydrogen bonds : bond 0.05780 / 3.82 ( 735) hydrogen bonds : angle 4.53610 / 3.11 ( 1811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 422 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8243 (mtp-110) REVERT: A 50 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 76 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: A 77 ASP cc_start: 0.8316 (p0) cc_final: 0.7876 (p0) REVERT: B 92 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.6444 (tpt-90) REVERT: D 60 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8714 (mtpp) REVERT: D 62 MET cc_start: 0.8117 (mmm) cc_final: 0.7903 (mmm) REVERT: D 79 GLU cc_start: 0.7395 (pp20) cc_final: 0.7028 (pp20) REVERT: D 82 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8249 (mmmt) REVERT: D 102 ARG cc_start: 0.8693 (mtp-110) cc_final: 0.8201 (ttp80) REVERT: E 83 ARG cc_start: 0.7334 (mmp80) cc_final: 0.6957 (mmp80) REVERT: F 44 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8444 (mtpp) REVERT: F 92 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8513 (tmt-80) REVERT: G 21 ARG cc_start: 0.8029 (ptt90) cc_final: 0.7683 (ppt170) REVERT: G 44 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7194 (ttp80) REVERT: G 92 ASP cc_start: 0.7295 (t0) cc_final: 0.7064 (t0) REVERT: H 96 GLU cc_start: 0.7960 (pm20) cc_final: 0.7479 (pm20) REVERT: K 233 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.3403 (p90) REVERT: K 252 CYS cc_start: 0.8203 (p) cc_final: 0.7491 (t) REVERT: K 276 MET cc_start: 0.7344 (tpp) cc_final: 0.7049 (tpp) REVERT: K 316 TYR cc_start: 0.4371 (m-10) cc_final: 0.4074 (m-10) REVERT: K 374 SER cc_start: 0.8446 (m) cc_final: 0.8095 (p) REVERT: K 398 LYS cc_start: 0.3334 (OUTLIER) cc_final: 0.2470 (pttm) REVERT: M 149 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5930 (pttp) REVERT: M 157 CYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6868 (p) REVERT: M 209 MET cc_start: 0.5441 (pp-130) cc_final: 0.5145 (pp-130) REVERT: M 215 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8230 (pp) REVERT: M 221 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6752 (mmtt) REVERT: M 237 GLN cc_start: 0.6767 (pm20) cc_final: 0.6193 (pm20) outliers start: 64 outliers final: 54 residues processed: 452 average time/residue: 0.1848 time to fit residues: 114.4226 Evaluate side-chains 480 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 418 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 285 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.111670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093844 restraints weight = 54591.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096101 restraints weight = 30133.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097604 restraints weight = 19820.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.098580 restraints weight = 14893.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099202 restraints weight = 12366.309| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.6741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.341 17881 Z= 0.258 Angle : 1.087 59.196 25382 Z= 0.594 Chirality : 0.056 0.784 2864 Planarity : 0.008 0.161 2198 Dihedral : 29.415 171.065 4771 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 5.25 % Allowed : 36.28 % Favored : 58.47 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.15 % 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: -3.47 (0.21), residues: 1323 helix: -1.62 (0.18), residues: 630 sheet: -1.82 (1.02), residues: 27 loop : -3.08 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.002 ARG B 45 TYR 0.032 0.003 TYR K 352 PHE 0.042 0.002 PHE M 217 TRP 0.014 0.002 TRP M 279 HIS 0.003 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.26 (17881) covalent geometry : angle 1.08748 / 0.59 (25382) hydrogen bonds : bond 0.05780 / 3.82 ( 735) hydrogen bonds : angle 4.53610 / 3.11 ( 1811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.95 seconds wall clock time: 58 minutes 10.44 seconds (3490.44 seconds total)