Starting phenix.real_space_refine on Sat Jul 4 12:24:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2z_38023/07_2026/8x2z_38023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2z_38023/07_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_38023/07_2026/8x2z_38023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2z_38023/07_2026/8x2z_38023.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x2z_38023/07_2026/8x2z_38023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2z_38023/07_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-dev-6108/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: 3.17, per 1000 atoms: 0.19 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: 1.07 Conformation dependent library (CDL) restraints added in 363.5 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: 2.00 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: 2.96 Time building geometry restraints manager: 1.45 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: 24410 3.02 - 6.04: 844 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- 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 : 1.355 15.093 25382 Z= 0.925 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 1.35509 / 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 : 0.479 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 51 ILE cc_start: 0.5781 (pp) cc_final: 0.5155 (pt) REVERT: A 106 ASP cc_start: 0.7028 (p0) cc_final: 0.6783 (p0) REVERT: B 85 ASP cc_start: 0.8226 (p0) cc_final: 0.8022 (p0) REVERT: C 67 LEU cc_start: 0.6408 (tp) cc_final: 0.6114 (tp) REVERT: D 74 GLU cc_start: 0.6997 (tp30) cc_final: 0.6681 (tp30) REVERT: D 83 LEU cc_start: 0.7602 (tm) cc_final: 0.7175 (mt) REVERT: E 50 GLU cc_start: 0.7104 (tp30) cc_final: 0.6684 (tp30) REVERT: F 87 VAL cc_start: 0.7766 (m) cc_final: 0.7481 (p) REVERT: G 67 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7661 (mm) REVERT: G 87 LEU cc_start: 0.8064 (pt) cc_final: 0.7715 (pt) REVERT: H 51 THR cc_start: 0.6711 (m) cc_final: 0.6192 (p) REVERT: H 74 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7384 (tp30) REVERT: H 93 SER cc_start: 0.8660 (t) cc_final: 0.8327 (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: 0.7174 (ttp80) REVERT: H 122 THR cc_start: 0.8059 (m) cc_final: 0.7226 (m) REVERT: H 123 LYS cc_start: 0.8249 (mppt) cc_final: 0.7991 (mppt) REVERT: K 274 TYR cc_start: 0.7178 (m-80) cc_final: 0.6886 (m-80) REVERT: K 289 TYR cc_start: 0.5299 (p90) cc_final: 0.4900 (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: 0.5798 (pp) REVERT: K 406 ASN cc_start: 0.6260 (m110) cc_final: 0.5586 (m-40) REVERT: L 34 GLN cc_start: 0.8393 (mm110) cc_final: 0.8177 (mp10) REVERT: M 169 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7324 (mt-10) REVERT: M 209 MET cc_start: 0.6033 (pp-130) cc_final: 0.5629 (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: 0.8251 (pp20) outliers start: 51 outliers final: 6 residues processed: 560 average time/residue: 0.1617 time to fit residues: 125.4677 Evaluate side-chains 449 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 440 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 59 GLN 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 ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 ASN M 258 GLN M 338 HIS M 363 ASN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.110893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093345 restraints weight = 53893.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095770 restraints weight = 27768.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.097381 restraints weight = 17399.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098430 restraints weight = 12605.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.099091 restraints weight = 10188.842| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17881 Z= 0.225 Angle : 1.021 15.053 25382 Z= 0.554 Chirality : 0.057 0.282 2864 Planarity : 0.008 0.120 2198 Dihedral : 30.057 172.208 4790 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.11 % Favored : 88.81 % Rotamer: Outliers : 7.17 % Allowed : 24.27 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.46 % 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: -2.61 (0.16), residues: 633 sheet: -2.04 (0.96), residues: 27 loop : -3.48 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 83 TYR 0.057 0.003 TYR D 86 PHE 0.025 0.003 PHE M 249 TRP 0.011 0.002 TRP M 279 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (17881) covalent geometry : angle 1.02123 / 0.55 (25382) hydrogen bonds : bond 0.06962 / 4.49 ( 735) hydrogen bonds : angle 4.91675 / 3.34 ( 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 561 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 475 time to evaluate : 0.480 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: 0.7004 (tpp-160) cc_final: 0.6460 (mmm160) REVERT: A 51 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7444 (pt) REVERT: A 52 ARG cc_start: 0.7373 (mtm110) cc_final: 0.6986 (mtm110) REVERT: A 53 ARG cc_start: 0.8320 (tmm-80) cc_final: 0.8108 (ptm-80) REVERT: A 59 GLU cc_start: 0.7846 (pp20) cc_final: 0.7332 (pp20) REVERT: A 105 GLU cc_start: 0.7810 (pp20) cc_final: 0.7369 (pp20) REVERT: B 34 ILE cc_start: 0.8437 (pp) cc_final: 0.8162 (pp) REVERT: B 36 ARG cc_start: 0.7649 (ttm110) cc_final: 0.6875 (mtm-85) REVERT: B 55 ARG cc_start: 0.8423 (mpp80) cc_final: 0.8041 (mtm-85) REVERT: C 37 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8309 (ttt-90) REVERT: C 63 GLU cc_start: 0.6399 (pm20) cc_final: 0.6036 (pm20) REVERT: C 79 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7293 (ttp80) REVERT: D 57 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7364 (tp) REVERT: D 74 GLU cc_start: 0.7005 (tp30) cc_final: 0.6664 (tp30) REVERT: D 79 GLU cc_start: 0.7077 (pp20) cc_final: 0.6852 (pp20) REVERT: D 86 TYR cc_start: 0.7621 (p90) cc_final: 0.7408 (p90) REVERT: D 96 GLU cc_start: 0.7188 (pp20) cc_final: 0.6765 (tm-30) REVERT: E 42 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6234 (pmmt) REVERT: F 60 SER cc_start: 0.7999 (m) cc_final: 0.7604 (t) REVERT: F 79 LYS cc_start: 0.7711 (ptmm) cc_final: 0.7048 (tppt) REVERT: F 87 VAL cc_start: 0.7869 (m) cc_final: 0.7598 (p) REVERT: G 24 LEU cc_start: 0.7990 (mm) cc_final: 0.7669 (mp) REVERT: G 34 TYR cc_start: 0.7609 (m-10) cc_final: 0.7194 (m-10) REVERT: H 51 THR cc_start: 0.6132 (m) cc_final: 0.5859 (p) REVERT: H 119 ARG cc_start: 0.7830 (ptm-80) cc_final: 0.7512 (ttt-90) REVERT: K 172 MET cc_start: 0.6555 (tmm) cc_final: 0.6084 (tmm) REVERT: K 210 GLN cc_start: 0.5886 (OUTLIER) cc_final: 0.5597 (pp30) REVERT: K 242 ARG cc_start: 0.7773 (tpt-90) cc_final: 0.7336 (tpt-90) REVERT: K 243 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (pmtt) REVERT: K 249 ARG cc_start: 0.2775 (ttt180) cc_final: 0.2139 (ttp80) REVERT: K 323 PHE cc_start: 0.7061 (t80) cc_final: 0.6618 (t80) REVERT: K 333 LYS cc_start: 0.8570 (tmtm) cc_final: 0.8188 (tmtm) REVERT: K 350 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.6804 (mmm-85) REVERT: K 379 MET cc_start: 0.5127 (tmt) cc_final: 0.4587 (tmt) REVERT: K 393 ILE cc_start: 0.5471 (OUTLIER) cc_final: 0.5266 (pp) REVERT: L 34 GLN cc_start: 0.8329 (mm110) cc_final: 0.8057 (mm-40) REVERT: M 133 TYR cc_start: 0.5009 (m-80) cc_final: 0.3996 (m-80) REVERT: M 197 GLU cc_start: 0.7851 (mp0) cc_final: 0.6259 (mp0) REVERT: M 209 MET cc_start: 0.5367 (pp-130) cc_final: 0.5060 (pp-130) REVERT: M 232 PHE cc_start: 0.6747 (p90) cc_final: 0.6358 (p90) REVERT: N 23 TYR cc_start: 0.5879 (m-80) cc_final: 0.5532 (m-80) REVERT: N 25 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6199 (tp) REVERT: N 31 ASN cc_start: 0.6397 (p0) cc_final: 0.6017 (p0) REVERT: N 32 ASP cc_start: 0.7982 (m-30) cc_final: 0.7740 (m-30) REVERT: N 85 GLU cc_start: 0.8593 (pp20) cc_final: 0.8234 (pp20) REVERT: N 86 LYS cc_start: 0.7480 (mttt) cc_final: 0.7192 (mtpp) outliers start: 86 outliers final: 44 residues processed: 513 average time/residue: 0.1631 time to fit residues: 116.0862 Evaluate side-chains 489 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 438 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE 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 83 ARG 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 57 ILE 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 124 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 126 LEU 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 83 ARG Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 44 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 66 ASN 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 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: 2.9990 chunk 136 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 116 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.0570 chunk 74 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN D 50 GLN D 59 GLN D 98 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN H 59 GLN H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 GLN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS K 406 ASN K 427 ASN M 198 HIS M 363 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.111891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094339 restraints weight = 54739.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096742 restraints weight = 28460.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.098323 restraints weight = 17953.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099366 restraints weight = 13139.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100022 restraints weight = 10649.970| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3877 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= 0.184 Angle : 0.938 16.460 25382 Z= 0.507 Chirality : 0.053 0.250 2864 Planarity : 0.007 0.136 2198 Dihedral : 29.775 170.256 4783 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 8.17 % Allowed : 26.52 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.38 % 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: -3.98 (0.20), residues: 1323 helix: -2.10 (0.18), residues: 641 sheet: -2.05 (0.95), residues: 27 loop : -3.29 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 83 TYR 0.073 0.003 TYR K 352 PHE 0.035 0.002 PHE M 217 TRP 0.036 0.003 TRP M 279 HIS 0.011 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (17881) covalent geometry : angle 0.93782 / 0.51 (25382) hydrogen bonds : bond 0.06269 / 4.08 ( 735) hydrogen bonds : angle 4.67976 / 3.20 ( 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 552 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 454 time to evaluate : 0.541 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: A 40 ARG cc_start: 0.7005 (tpp-160) cc_final: 0.6643 (mmm160) REVERT: A 50 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7629 (mt-10) REVERT: A 53 ARG cc_start: 0.8329 (tmm-80) cc_final: 0.8086 (ptm-80) REVERT: A 59 GLU cc_start: 0.7921 (pp20) cc_final: 0.7470 (pp20) REVERT: A 60 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6104 (tp) REVERT: A 64 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8236 (mmmm) REVERT: B 31 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7746 (ttpp) REVERT: B 34 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8157 (pp) REVERT: B 55 ARG cc_start: 0.8495 (mpp80) cc_final: 0.8173 (mtm-85) REVERT: C 21 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5039 (ttp80) REVERT: C 32 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7892 (ttmm) REVERT: C 63 GLU cc_start: 0.6367 (pm20) cc_final: 0.6087 (pm20) REVERT: D 57 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7428 (tp) REVERT: D 73 PHE cc_start: 0.8492 (t80) cc_final: 0.8292 (t80) REVERT: D 74 GLU cc_start: 0.6988 (tp30) cc_final: 0.6655 (tp30) REVERT: E 42 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.6050 (pmmt) REVERT: E 122 LYS cc_start: 0.7269 (pptt) cc_final: 0.7059 (ptmm) REVERT: F 60 SER cc_start: 0.7950 (m) cc_final: 0.7638 (t) REVERT: F 79 LYS cc_start: 0.7585 (ptmm) cc_final: 0.7271 (ttpt) REVERT: F 87 VAL cc_start: 0.7995 (m) cc_final: 0.7715 (p) REVERT: F 95 ARG cc_start: 0.6588 (pmm-80) cc_final: 0.6286 (ptt-90) REVERT: G 24 LEU cc_start: 0.7907 (mm) cc_final: 0.7617 (mp) REVERT: H 51 THR cc_start: 0.6485 (m) cc_final: 0.6236 (p) REVERT: H 97 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8574 (tt) REVERT: K 172 MET cc_start: 0.6631 (tmm) cc_final: 0.6283 (tmm) REVERT: K 243 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8052 (pmtt) REVERT: K 329 LYS cc_start: 0.7726 (mttm) cc_final: 0.7383 (mtpp) REVERT: K 333 LYS cc_start: 0.8617 (tmtm) cc_final: 0.8165 (tmtm) REVERT: K 379 MET cc_start: 0.5238 (tmt) cc_final: 0.4457 (tmt) REVERT: L 29 PHE cc_start: 0.5962 (m-80) cc_final: 0.5544 (m-80) REVERT: L 34 GLN cc_start: 0.8392 (mm110) cc_final: 0.8154 (mm-40) REVERT: M 169 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7340 (mt-10) REVERT: M 209 MET cc_start: 0.5279 (pp-130) cc_final: 0.4974 (pp-130) REVERT: M 232 PHE cc_start: 0.6647 (p90) cc_final: 0.6303 (p90) REVERT: M 242 ILE cc_start: 0.6404 (mm) cc_final: 0.6052 (mm) REVERT: N 31 ASN cc_start: 0.6041 (p0) cc_final: 0.5671 (p0) REVERT: N 32 ASP cc_start: 0.7960 (m-30) cc_final: 0.7695 (m-30) REVERT: N 85 GLU cc_start: 0.8601 (pp20) cc_final: 0.8293 (pp20) REVERT: N 86 LYS cc_start: 0.7452 (mttt) cc_final: 0.7187 (mtpp) outliers start: 98 outliers final: 50 residues processed: 499 average time/residue: 0.1719 time to fit residues: 119.3479 Evaluate side-chains 487 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 430 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 34 ILE 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 21 ARG Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 ARG 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 57 ILE 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 50 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 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 83 ARG Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE 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 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 272 LEU 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 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 M residue 363 ASN 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: 0.9980 chunk 54 optimal weight: 0.3980 chunk 95 optimal weight: 0.0870 chunk 44 optimal weight: 0.0570 chunk 51 optimal weight: 0.3980 chunk 130 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 59 GLN H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS K 406 ASN M 258 GLN ** N 12 GLN ** 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 = 0.3901 r_free = 0.3901 target = 0.112415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094991 restraints weight = 54854.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097414 restraints weight = 28701.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098992 restraints weight = 18256.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.100010 restraints weight = 13397.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100666 restraints weight = 10908.808| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17881 Z= 0.177 Angle : 0.909 17.766 25382 Z= 0.491 Chirality : 0.052 0.323 2864 Planarity : 0.007 0.132 2198 Dihedral : 29.611 169.403 4779 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 7.51 % Allowed : 27.44 % Favored : 65.05 % 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: -3.75 (0.20), residues: 1323 helix: -1.82 (0.18), residues: 645 sheet: -2.01 (0.92), residues: 27 loop : -3.27 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 44 TYR 0.046 0.003 TYR N 23 PHE 0.029 0.002 PHE L 29 TRP 0.028 0.002 TRP M 279 HIS 0.007 0.001 HIS K 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (17881) covalent geometry : angle 0.90931 / 0.49 (25382) hydrogen bonds : bond 0.05814 / 3.78 ( 735) hydrogen bonds : angle 4.55225 / 3.11 ( 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 538 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 448 time to evaluate : 0.510 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 40 ARG cc_start: 0.7047 (tpp-160) cc_final: 0.6774 (mmm160) REVERT: A 59 GLU cc_start: 0.7873 (pp20) cc_final: 0.7512 (pp20) REVERT: A 60 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6170 (tp) REVERT: A 64 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8447 (mmmm) REVERT: A 97 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7100 (tt0) REVERT: B 31 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7852 (ttpp) REVERT: B 34 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8172 (pp) REVERT: B 55 ARG cc_start: 0.8482 (mpp80) cc_final: 0.8239 (mtt-85) REVERT: C 21 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.4930 (ttp80) REVERT: C 32 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7993 (ttmm) REVERT: C 63 GLU cc_start: 0.6306 (pm20) cc_final: 0.5839 (pm20) REVERT: D 46 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7113 (pptt) REVERT: D 59 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7366 (mp-120) REVERT: D 74 GLU cc_start: 0.7032 (tp30) cc_final: 0.6596 (tp30) REVERT: D 79 GLU cc_start: 0.7384 (pp20) cc_final: 0.7158 (pp20) REVERT: D 86 TYR cc_start: 0.7696 (p90) cc_final: 0.7102 (p90) REVERT: D 91 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8111 (t) REVERT: E 42 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6231 (pmmt) REVERT: F 60 SER cc_start: 0.7960 (m) cc_final: 0.7678 (t) REVERT: F 87 VAL cc_start: 0.8013 (m) cc_final: 0.7770 (p) REVERT: H 49 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7253 (tmmt) REVERT: H 51 THR cc_start: 0.6615 (m) cc_final: 0.6316 (p) REVERT: K 249 ARG cc_start: 0.3040 (ttt-90) cc_final: 0.2276 (ttp80) REVERT: K 287 VAL cc_start: 0.5653 (OUTLIER) cc_final: 0.5447 (m) REVERT: K 321 ILE cc_start: 0.8632 (tt) cc_final: 0.8328 (tp) REVERT: K 322 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: K 333 LYS cc_start: 0.8599 (tmtm) cc_final: 0.8212 (tmtm) REVERT: K 373 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8383 (mp) REVERT: M 209 MET cc_start: 0.5360 (pp-130) cc_final: 0.5079 (pp-130) REVERT: M 232 PHE cc_start: 0.6587 (p90) cc_final: 0.5584 (p90) REVERT: N 22 ARG cc_start: 0.7521 (mmm160) cc_final: 0.6888 (mmm160) REVERT: N 85 GLU cc_start: 0.8598 (pp20) cc_final: 0.8067 (pp20) REVERT: N 86 LYS cc_start: 0.7419 (mttt) cc_final: 0.7158 (mtpp) outliers start: 90 outliers final: 49 residues processed: 486 average time/residue: 0.1690 time to fit residues: 114.3071 Evaluate side-chains 482 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 423 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR 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 B residue 34 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 83 ARG 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 46 LYS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 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 66 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 87 LEU 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 121 VAL Chi-restraints excluded: chain K residue 214 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 286 LEU Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain M residue 141 PHE Chi-restraints excluded: chain M residue 163 ASN 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 24 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 0.0030 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 27 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS K 406 ASN M 243 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.112755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095613 restraints weight = 54082.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097852 restraints weight = 29151.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099363 restraints weight = 18909.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100312 restraints weight = 14029.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100936 restraints weight = 11575.028| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17881 Z= 0.176 Angle : 0.911 17.465 25382 Z= 0.486 Chirality : 0.051 0.242 2864 Planarity : 0.006 0.119 2198 Dihedral : 29.479 169.370 4777 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 7.67 % Allowed : 28.44 % Favored : 63.89 % 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: -3.65 (0.20), residues: 1323 helix: -1.71 (0.19), residues: 645 sheet: -1.87 (0.96), residues: 27 loop : -3.28 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 83 TYR 0.032 0.002 TYR M 133 PHE 0.039 0.002 PHE M 217 TRP 0.031 0.003 TRP M 279 HIS 0.004 0.001 HIS M 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (17881) covalent geometry : angle 0.91075 / 0.49 (25382) hydrogen bonds : bond 0.05738 / 3.72 ( 735) hydrogen bonds : angle 4.49312 / 3.08 ( 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 529 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 437 time to evaluate : 0.490 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: 0.7077 (tpp-160) cc_final: 0.6770 (mmm160) REVERT: A 50 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 59 GLU cc_start: 0.7931 (pp20) cc_final: 0.7616 (pp20) REVERT: A 60 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.5701 (tp) REVERT: A 64 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8346 (mmmm) REVERT: A 97 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7065 (tt0) REVERT: A 106 ASP cc_start: 0.7365 (p0) cc_final: 0.7150 (p0) REVERT: A 123 ASP cc_start: 0.7116 (m-30) cc_final: 0.6755 (m-30) REVERT: A 125 LYS cc_start: 0.7974 (ptmm) cc_final: 0.7587 (ptmm) REVERT: A 131 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8470 (mtt180) REVERT: B 31 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7950 (ttpp) REVERT: B 55 ARG cc_start: 0.8464 (mpp80) cc_final: 0.7964 (mtt-85) REVERT: C 21 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5440 (ppp-140) REVERT: D 57 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7368 (mp) REVERT: D 59 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7358 (mp-120) REVERT: D 74 GLU cc_start: 0.7083 (tp30) cc_final: 0.6629 (tp30) REVERT: D 86 TYR cc_start: 0.7739 (p90) cc_final: 0.7057 (p90) REVERT: E 42 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6185 (pmmt) REVERT: E 121 LYS cc_start: 0.8223 (mptt) cc_final: 0.7897 (mptt) REVERT: F 36 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6801 (mtt90) REVERT: F 53 GLU cc_start: 0.7504 (pm20) cc_final: 0.6724 (pm20) REVERT: F 60 SER cc_start: 0.7977 (m) cc_final: 0.7737 (t) REVERT: F 87 VAL cc_start: 0.8052 (m) cc_final: 0.7814 (p) REVERT: H 46 LYS cc_start: 0.8260 (tttm) cc_final: 0.7849 (tttp) REVERT: H 49 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7324 (tmmt) REVERT: H 51 THR cc_start: 0.6702 (m) cc_final: 0.6373 (p) REVERT: H 96 GLU cc_start: 0.8247 (pm20) cc_final: 0.8025 (pm20) REVERT: K 249 ARG cc_start: 0.3093 (ttt-90) cc_final: 0.2373 (ttp80) REVERT: K 287 VAL cc_start: 0.5854 (OUTLIER) cc_final: 0.5572 (m) REVERT: K 321 ILE cc_start: 0.8178 (tt) cc_final: 0.7819 (tp) REVERT: K 329 LYS cc_start: 0.7714 (mttm) cc_final: 0.7474 (mtpp) REVERT: K 333 LYS cc_start: 0.8670 (tmtm) cc_final: 0.8202 (tmtm) REVERT: K 350 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7508 (mmm-85) REVERT: M 155 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7403 (mm-30) REVERT: M 167 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4093 (pmt-80) REVERT: M 197 GLU cc_start: 0.8252 (mm-30) cc_final: 0.6345 (mm-30) REVERT: M 209 MET cc_start: 0.5363 (pp-130) cc_final: 0.5090 (pp-130) REVERT: M 354 ARG cc_start: 0.6898 (tpm170) cc_final: 0.6691 (tpm170) REVERT: N 25 LEU cc_start: 0.6395 (mm) cc_final: 0.6128 (tp) REVERT: N 85 GLU cc_start: 0.8559 (pp20) cc_final: 0.7922 (pp20) outliers start: 92 outliers final: 45 residues processed: 480 average time/residue: 0.1725 time to fit residues: 113.4856 Evaluate side-chains 478 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 425 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 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 21 ARG Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 ARG 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 57 ILE 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 42 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 50 ILE 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 54 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 87 LEU 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 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 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 301 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 110 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: 0.9990 chunk 140 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** 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 K 406 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.112751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095603 restraints weight = 54538.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097860 restraints weight = 29210.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099354 restraints weight = 18889.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100333 restraints weight = 14056.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100922 restraints weight = 11579.836| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17881 Z= 0.185 Angle : 0.920 17.586 25382 Z= 0.493 Chirality : 0.051 0.246 2864 Planarity : 0.008 0.170 2198 Dihedral : 29.442 169.186 4773 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 6.34 % Allowed : 30.61 % Favored : 63.05 % 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: -3.60 (0.20), residues: 1323 helix: -1.70 (0.18), residues: 646 sheet: -1.61 (1.01), residues: 27 loop : -3.22 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 52 TYR 0.038 0.002 TYR N 23 PHE 0.038 0.003 PHE M 217 TRP 0.025 0.002 TRP M 279 HIS 0.004 0.001 HIS K 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (17881) covalent geometry : angle 0.91959 / 0.49 (25382) hydrogen bonds : bond 0.05799 / 3.77 ( 735) hydrogen bonds : angle 4.43501 / 3.04 ( 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 519 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 443 time to evaluate : 0.505 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: A 50 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 60 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6161 (tp) REVERT: A 97 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6988 (tt0) REVERT: A 105 GLU cc_start: 0.7940 (pp20) cc_final: 0.7689 (pp20) REVERT: A 120 GLN cc_start: 0.6951 (mp10) cc_final: 0.6441 (mp10) REVERT: A 125 LYS cc_start: 0.8044 (ptmm) cc_final: 0.7717 (ptmm) REVERT: A 131 ARG cc_start: 0.8793 (mtp85) cc_final: 0.8491 (mtt-85) REVERT: B 31 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8020 (ttpp) REVERT: C 21 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5176 (ppp-140) REVERT: C 63 GLU cc_start: 0.6731 (pm20) cc_final: 0.6413 (pm20) REVERT: D 59 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7329 (mp-120) REVERT: D 74 GLU cc_start: 0.7121 (tp30) cc_final: 0.6638 (tp30) REVERT: D 82 LYS cc_start: 0.8473 (mtpp) cc_final: 0.7989 (mtpp) REVERT: D 83 LEU cc_start: 0.8603 (mt) cc_final: 0.8202 (mt) REVERT: D 86 TYR cc_start: 0.7766 (p90) cc_final: 0.7054 (p90) REVERT: D 111 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7301 (mtmm) REVERT: E 42 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6205 (pmmt) REVERT: E 94 GLU cc_start: 0.7590 (tt0) cc_final: 0.6890 (tp30) REVERT: F 36 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6735 (mtt90) REVERT: F 53 GLU cc_start: 0.7438 (pm20) cc_final: 0.7228 (pm20) REVERT: G 94 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7993 (mm-30) REVERT: H 46 LYS cc_start: 0.8311 (tttm) cc_final: 0.7980 (tmtt) REVERT: H 51 THR cc_start: 0.6887 (m) cc_final: 0.6552 (p) REVERT: H 96 GLU cc_start: 0.8143 (pm20) cc_final: 0.7877 (pm20) REVERT: K 192 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6555 (pm20) REVERT: K 287 VAL cc_start: 0.5834 (OUTLIER) cc_final: 0.5540 (m) REVERT: K 301 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7111 (p0) REVERT: K 321 ILE cc_start: 0.8599 (tt) cc_final: 0.8372 (tp) REVERT: K 329 LYS cc_start: 0.7663 (mttm) cc_final: 0.7461 (mtpp) REVERT: K 333 LYS cc_start: 0.8703 (tmtm) cc_final: 0.8321 (tmtm) REVERT: K 350 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: K 398 LYS cc_start: 0.3631 (OUTLIER) cc_final: 0.3278 (pttm) REVERT: M 167 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.4036 (pmt-80) REVERT: M 168 ASP cc_start: 0.7280 (p0) cc_final: 0.7017 (p0) REVERT: M 209 MET cc_start: 0.5406 (pp-130) cc_final: 0.5147 (pp-130) REVERT: M 335 ARG cc_start: 0.6192 (tpt90) cc_final: 0.5981 (tpt90) REVERT: N 22 ARG cc_start: 0.7234 (mmm160) cc_final: 0.7009 (mmm160) REVERT: N 31 ASN cc_start: 0.6013 (p0) cc_final: 0.4819 (p0) REVERT: N 32 ASP cc_start: 0.7819 (m-30) cc_final: 0.7505 (m-30) REVERT: N 85 GLU cc_start: 0.8603 (pp20) cc_final: 0.8001 (pp20) outliers start: 76 outliers final: 45 residues processed: 474 average time/residue: 0.1714 time to fit residues: 112.1543 Evaluate side-chains 477 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 424 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 124 ILE 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 67 LEU Chi-restraints excluded: chain C residue 83 ARG 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 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 36 ARG 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 54 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 87 LEU 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 K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 301 ASN Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** 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 K 406 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.112935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095787 restraints weight = 54321.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098033 restraints weight = 29418.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.099541 restraints weight = 19012.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100519 restraints weight = 14091.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.101124 restraints weight = 11595.672| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17881 Z= 0.186 Angle : 0.933 15.838 25382 Z= 0.497 Chirality : 0.052 0.249 2864 Planarity : 0.007 0.159 2198 Dihedral : 29.405 168.836 4769 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 6.84 % Allowed : 32.36 % Favored : 60.80 % 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: -3.52 (0.20), residues: 1323 helix: -1.65 (0.19), residues: 638 sheet: -1.14 (1.10), residues: 22 loop : -3.16 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG G 44 TYR 0.028 0.002 TYR M 278 PHE 0.038 0.002 PHE M 217 TRP 0.031 0.002 TRP M 279 HIS 0.003 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (17881) covalent geometry : angle 0.93308 / 0.50 (25382) hydrogen bonds : bond 0.05766 / 3.77 ( 735) hydrogen bonds : angle 4.47188 / 3.09 ( 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 520 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 438 time to evaluate : 0.385 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 50 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 60 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6465 (tp) REVERT: A 97 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7053 (tt0) REVERT: A 105 GLU cc_start: 0.7943 (pp20) cc_final: 0.7677 (pp20) REVERT: A 106 ASP cc_start: 0.7487 (p0) cc_final: 0.7222 (p0) REVERT: A 120 GLN cc_start: 0.7102 (mp10) cc_final: 0.6689 (mp10) REVERT: A 125 LYS cc_start: 0.8129 (ptmm) cc_final: 0.7796 (ptmm) REVERT: A 131 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8546 (mtt-85) REVERT: B 31 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8133 (ttpp) REVERT: C 21 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5423 (ppp-140) REVERT: C 63 GLU cc_start: 0.6715 (pm20) cc_final: 0.6432 (pm20) REVERT: D 46 LYS cc_start: 0.7927 (pptt) cc_final: 0.7630 (pptt) REVERT: D 57 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7327 (mp) REVERT: D 59 GLN cc_start: 0.7690 (tp-100) cc_final: 0.7246 (mp-120) REVERT: D 74 GLU cc_start: 0.7182 (tp30) cc_final: 0.6684 (tp30) REVERT: D 82 LYS cc_start: 0.8468 (mtpp) cc_final: 0.7791 (mmmt) REVERT: D 86 TYR cc_start: 0.7825 (p90) cc_final: 0.7137 (p90) REVERT: D 88 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8642 (tppt) REVERT: D 111 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7474 (mtmm) REVERT: E 42 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6236 (pmmt) REVERT: E 94 GLU cc_start: 0.7548 (tt0) cc_final: 0.7000 (tp30) REVERT: F 36 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6807 (mtt90) REVERT: F 53 GLU cc_start: 0.7344 (pm20) cc_final: 0.7124 (pm20) REVERT: G 38 HIS cc_start: 0.6973 (t70) cc_final: 0.6584 (t-90) REVERT: G 92 ASP cc_start: 0.7217 (t0) cc_final: 0.6895 (t0) REVERT: H 46 LYS cc_start: 0.8354 (tttm) cc_final: 0.7875 (tttm) REVERT: H 49 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7377 (tmmt) REVERT: H 51 THR cc_start: 0.7031 (m) cc_final: 0.6588 (p) REVERT: H 96 GLU cc_start: 0.8141 (pm20) cc_final: 0.7778 (pm20) REVERT: K 192 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6789 (pm20) REVERT: K 233 TYR cc_start: 0.5093 (OUTLIER) cc_final: 0.3164 (p90) REVERT: K 287 VAL cc_start: 0.5632 (OUTLIER) cc_final: 0.5319 (m) REVERT: K 321 ILE cc_start: 0.8643 (tt) cc_final: 0.8441 (tp) REVERT: K 333 LYS cc_start: 0.8740 (tmtm) cc_final: 0.8363 (tmtm) REVERT: K 350 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7499 (mmm-85) REVERT: K 398 LYS cc_start: 0.3635 (OUTLIER) cc_final: 0.2959 (pttm) REVERT: M 167 ARG cc_start: 0.5344 (OUTLIER) cc_final: 0.4037 (pmt-80) REVERT: M 168 ASP cc_start: 0.7095 (p0) cc_final: 0.6876 (p0) REVERT: M 209 MET cc_start: 0.5376 (pp-130) cc_final: 0.5120 (pp-130) REVERT: N 85 GLU cc_start: 0.8610 (pp20) cc_final: 0.7999 (pp20) REVERT: N 86 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7497 (mmmt) outliers start: 82 outliers final: 46 residues processed: 479 average time/residue: 0.1665 time to fit residues: 110.1113 Evaluate side-chains 481 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 425 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 58 THR 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 A residue 124 ILE 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 67 LEU Chi-restraints excluded: chain C residue 81 THR 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 57 ILE 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 61 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 36 ARG 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 54 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 84 HIS 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 123 LYS Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 398 LYS 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 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 142 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 52 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 HIS ** N 102 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 = 0.3912 r_free = 0.3912 target = 0.112883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095635 restraints weight = 54779.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097826 restraints weight = 30236.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099307 restraints weight = 19876.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.100277 restraints weight = 14898.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100898 restraints weight = 12298.239| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5919 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= 0.190 Angle : 0.960 16.187 25382 Z= 0.505 Chirality : 0.052 0.262 2864 Planarity : 0.008 0.186 2198 Dihedral : 29.379 169.516 4765 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 6.17 % Allowed : 33.53 % Favored : 60.30 % 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: -3.54 (0.20), residues: 1323 helix: -1.68 (0.18), residues: 646 sheet: -1.56 (1.04), residues: 27 loop : -3.16 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 83 TYR 0.043 0.003 TYR N 23 PHE 0.045 0.003 PHE K 323 TRP 0.025 0.002 TRP M 279 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17881) covalent geometry : angle 0.95959 / 0.51 (25382) hydrogen bonds : bond 0.05902 / 3.87 ( 735) hydrogen bonds : angle 4.52213 / 3.11 ( 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 520 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 446 time to evaluate : 0.593 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: A 50 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 72 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7722 (mtt90) REVERT: A 94 GLU cc_start: 0.7822 (tp30) cc_final: 0.7471 (tp30) REVERT: A 105 GLU cc_start: 0.7935 (pp20) cc_final: 0.7699 (pp20) REVERT: A 120 GLN cc_start: 0.7373 (mp10) cc_final: 0.7054 (mp10) REVERT: A 125 LYS cc_start: 0.8214 (ptmm) cc_final: 0.7933 (ptmm) REVERT: A 129 ARG cc_start: 0.7733 (tmt-80) cc_final: 0.7515 (tmt-80) REVERT: C 21 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.5667 (ppp-140) REVERT: C 63 GLU cc_start: 0.6804 (pm20) cc_final: 0.6486 (pm20) REVERT: D 59 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7215 (mp-120) REVERT: D 74 GLU cc_start: 0.7192 (tp30) cc_final: 0.6618 (tp30) REVERT: D 79 GLU cc_start: 0.7427 (pp20) cc_final: 0.7221 (pp20) REVERT: D 82 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8223 (mmmt) REVERT: D 111 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7501 (mtmm) REVERT: E 94 GLU cc_start: 0.7571 (tt0) cc_final: 0.7122 (tp30) REVERT: F 36 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6764 (mtt90) REVERT: F 44 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8372 (mtpp) REVERT: G 21 ARG cc_start: 0.8188 (pmt-80) cc_final: 0.7893 (ppt170) REVERT: G 38 HIS cc_start: 0.7096 (t70) cc_final: 0.6677 (t70) REVERT: H 46 LYS cc_start: 0.8378 (tttm) cc_final: 0.8114 (tttm) REVERT: H 51 THR cc_start: 0.7078 (m) cc_final: 0.6752 (p) REVERT: H 74 GLU cc_start: 0.7749 (tp30) cc_final: 0.7276 (tp30) REVERT: K 233 TYR cc_start: 0.5200 (OUTLIER) cc_final: 0.3475 (p90) REVERT: K 236 PHE cc_start: 0.7228 (p90) cc_final: 0.7001 (p90) REVERT: K 287 VAL cc_start: 0.5670 (OUTLIER) cc_final: 0.5386 (m) REVERT: K 333 LYS cc_start: 0.8721 (tmtm) cc_final: 0.8340 (tmtm) REVERT: K 350 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7509 (mmm-85) REVERT: K 398 LYS cc_start: 0.3578 (OUTLIER) cc_final: 0.2406 (pttp) REVERT: M 167 ARG cc_start: 0.5336 (OUTLIER) cc_final: 0.4043 (pmt-80) REVERT: M 168 ASP cc_start: 0.6969 (p0) cc_final: 0.6738 (p0) REVERT: M 169 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7326 (mt-10) REVERT: M 209 MET cc_start: 0.5338 (pp-130) cc_final: 0.5074 (pp-130) REVERT: N 31 ASN cc_start: 0.5124 (p0) cc_final: 0.4665 (p0) REVERT: N 85 GLU cc_start: 0.8680 (pp20) cc_final: 0.8163 (pp20) outliers start: 74 outliers final: 54 residues processed: 476 average time/residue: 0.1736 time to fit residues: 113.5873 Evaluate side-chains 493 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 433 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL 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 67 LEU Chi-restraints excluded: chain C residue 81 THR 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 E residue 61 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 52 GLU 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 24 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 60 LEU 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 87 LEU 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 K residue 165 ARG Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 398 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 197 GLU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU 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: 0.6980 chunk 12 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 156 optimal weight: 10.0000 chunk 36 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 98 GLN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3921 r_free = 0.3921 target = 0.113408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095775 restraints weight = 54482.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098096 restraints weight = 29830.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.099616 restraints weight = 19494.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.100616 restraints weight = 14553.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101249 restraints weight = 12011.547| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17881 Z= 0.190 Angle : 0.973 16.231 25382 Z= 0.512 Chirality : 0.051 0.272 2864 Planarity : 0.007 0.158 2198 Dihedral : 29.314 170.146 4765 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 5.59 % Allowed : 34.28 % Favored : 60.13 % 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: -3.47 (0.21), residues: 1323 helix: -1.67 (0.18), residues: 647 sheet: -1.77 (0.99), residues: 27 loop : -3.06 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 83 TYR 0.035 0.002 TYR C 52 PHE 0.056 0.003 PHE E 67 TRP 0.023 0.002 TRP M 279 HIS 0.003 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17881) covalent geometry : angle 0.97319 / 0.51 (25382) hydrogen bonds : bond 0.05700 / 3.74 ( 735) hydrogen bonds : angle 4.53012 / 3.13 ( 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 511 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 444 time to evaluate : 0.469 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: A 50 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 97 GLU cc_start: 0.7170 (tt0) cc_final: 0.6961 (tt0) REVERT: A 105 GLU cc_start: 0.7974 (pp20) cc_final: 0.7707 (pp20) REVERT: A 120 GLN cc_start: 0.7431 (mp10) cc_final: 0.7103 (mp10) REVERT: A 125 LYS cc_start: 0.8239 (ptmm) cc_final: 0.7975 (ptmm) REVERT: C 21 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5998 (ppp-140) REVERT: D 79 GLU cc_start: 0.7470 (pp20) cc_final: 0.7201 (pp20) REVERT: D 82 LYS cc_start: 0.8495 (mtpp) cc_final: 0.7939 (mmmt) REVERT: D 86 TYR cc_start: 0.7779 (p90) cc_final: 0.7032 (p90) REVERT: D 111 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7554 (mtmm) REVERT: E 66 PRO cc_start: 0.8011 (Cg_exo) cc_final: 0.7575 (Cg_endo) REVERT: E 94 GLU cc_start: 0.7499 (tt0) cc_final: 0.7010 (tp30) REVERT: F 36 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6802 (mtt90) REVERT: F 44 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8402 (mtpp) REVERT: F 50 ILE cc_start: 0.8439 (pt) cc_final: 0.8118 (mm) REVERT: G 21 ARG cc_start: 0.8195 (pmt-80) cc_final: 0.7919 (ppt170) REVERT: G 37 ARG cc_start: 0.7028 (ttp80) cc_final: 0.6789 (mtp85) REVERT: G 38 HIS cc_start: 0.7180 (t70) cc_final: 0.6736 (t70) REVERT: H 46 LYS cc_start: 0.8335 (tttm) cc_final: 0.7877 (tttm) REVERT: H 49 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7376 (tmmt) REVERT: H 51 THR cc_start: 0.7079 (m) cc_final: 0.6586 (p) REVERT: H 102 ARG cc_start: 0.8640 (ptm160) cc_final: 0.8426 (ptm160) REVERT: H 119 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7407 (tmm-80) REVERT: H 123 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7824 (mppt) REVERT: K 188 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7087 (tm-30) REVERT: K 233 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.3097 (p90) REVERT: K 252 CYS cc_start: 0.8118 (p) cc_final: 0.7442 (t) REVERT: K 319 LEU cc_start: 0.8608 (pt) cc_final: 0.7876 (mp) REVERT: K 333 LYS cc_start: 0.8773 (tmtm) cc_final: 0.8362 (tmtm) REVERT: K 398 LYS cc_start: 0.3252 (OUTLIER) cc_final: 0.2988 (pttp) REVERT: L 34 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8054 (mp10) REVERT: M 167 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4102 (pmt-80) REVERT: M 168 ASP cc_start: 0.7074 (p0) cc_final: 0.6781 (p0) REVERT: M 209 MET cc_start: 0.5301 (pp-130) cc_final: 0.5028 (pp-130) REVERT: M 237 GLN cc_start: 0.6902 (pm20) cc_final: 0.6574 (pm20) REVERT: M 285 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5729 (mp0) REVERT: N 85 GLU cc_start: 0.8818 (pp20) cc_final: 0.8261 (pp20) outliers start: 67 outliers final: 48 residues processed: 475 average time/residue: 0.1576 time to fit residues: 103.1113 Evaluate side-chains 489 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 433 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE 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 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 81 THR 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 97 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 91 LYS 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 24 LEU Chi-restraints excluded: chain G residue 54 THR 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 99 THR Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain K residue 165 ARG 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 358 ILE Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 398 LYS 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 172 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 285 GLU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 0.0370 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 81 optimal weight: 0.0030 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS K 301 ASN ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3934 r_free = 0.3934 target = 0.114273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096949 restraints weight = 54578.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099185 restraints weight = 30459.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.100643 restraints weight = 20150.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101620 restraints weight = 15194.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102234 restraints weight = 12598.548| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17881 Z= 0.185 Angle : 0.998 21.554 25382 Z= 0.519 Chirality : 0.051 0.269 2864 Planarity : 0.007 0.103 2198 Dihedral : 29.266 171.327 4765 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 5.42 % Allowed : 34.53 % Favored : 60.05 % 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: -3.42 (0.21), residues: 1323 helix: -1.68 (0.18), residues: 640 sheet: -1.98 (0.91), residues: 27 loop : -2.95 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 235 TYR 0.051 0.003 TYR K 352 PHE 0.069 0.003 PHE M 232 TRP 0.026 0.002 TRP M 279 HIS 0.005 0.001 HIS M 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (17881) covalent geometry : angle 0.99775 / 0.52 (25382) hydrogen bonds : bond 0.05673 / 3.71 ( 735) hydrogen bonds : angle 4.58626 / 3.18 ( 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 493 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 428 time to evaluate : 0.328 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: A 50 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 69 ARG cc_start: 0.7501 (ptp-170) cc_final: 0.7298 (ptt180) REVERT: A 72 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7626 (mtt90) REVERT: A 76 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: A 105 GLU cc_start: 0.8032 (pp20) cc_final: 0.7791 (pp20) REVERT: A 106 ASP cc_start: 0.7625 (p0) cc_final: 0.7340 (p0) REVERT: A 120 GLN cc_start: 0.7467 (mp10) cc_final: 0.7050 (mp10) REVERT: A 125 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7923 (ptmm) REVERT: A 131 ARG cc_start: 0.8785 (mtp85) cc_final: 0.8556 (mtt180) REVERT: C 21 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5868 (ppp-140) REVERT: C 79 ARG cc_start: 0.8020 (tmm-80) cc_final: 0.7807 (ttp80) REVERT: D 79 GLU cc_start: 0.7508 (pp20) cc_final: 0.7189 (pp20) REVERT: D 82 LYS cc_start: 0.8491 (mtpp) cc_final: 0.7949 (mmmt) REVERT: D 86 TYR cc_start: 0.7735 (p90) cc_final: 0.6989 (p90) REVERT: D 111 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7563 (mtmm) REVERT: E 94 GLU cc_start: 0.7415 (tt0) cc_final: 0.6933 (tp30) REVERT: F 36 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6856 (mtt90) REVERT: F 44 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8416 (mtpp) REVERT: F 50 ILE cc_start: 0.8304 (pt) cc_final: 0.8058 (mm) REVERT: F 55 ARG cc_start: 0.7656 (ptp-170) cc_final: 0.7430 (ptp-170) REVERT: F 84 LEU cc_start: 0.7900 (tp) cc_final: 0.7658 (tt) REVERT: F 91 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (ttpp) REVERT: G 21 ARG cc_start: 0.8144 (pmt-80) cc_final: 0.7828 (ppt170) REVERT: G 38 HIS cc_start: 0.7264 (t70) cc_final: 0.6795 (t70) REVERT: G 44 ARG cc_start: 0.7737 (tmm160) cc_final: 0.7384 (tmm160) REVERT: G 92 ASP cc_start: 0.7249 (t0) cc_final: 0.6877 (t0) REVERT: H 46 LYS cc_start: 0.8349 (tttm) cc_final: 0.8121 (tttm) REVERT: H 51 THR cc_start: 0.7119 (m) cc_final: 0.6644 (p) REVERT: H 119 ARG cc_start: 0.8126 (tmm-80) cc_final: 0.7188 (tmm-80) REVERT: H 123 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7754 (mppt) REVERT: K 188 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7052 (tm-30) REVERT: K 233 TYR cc_start: 0.5087 (OUTLIER) cc_final: 0.3070 (p90) REVERT: K 236 PHE cc_start: 0.7287 (p90) cc_final: 0.7050 (p90) REVERT: K 252 CYS cc_start: 0.8048 (p) cc_final: 0.7425 (t) REVERT: K 276 MET cc_start: 0.7139 (tpp) cc_final: 0.6774 (tpp) REVERT: K 333 LYS cc_start: 0.8743 (tmtm) cc_final: 0.8396 (tmtm) REVERT: K 398 LYS cc_start: 0.3379 (OUTLIER) cc_final: 0.3000 (pttp) REVERT: M 155 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7781 (mm-30) REVERT: M 167 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4274 (pmt-80) REVERT: M 168 ASP cc_start: 0.6889 (p0) cc_final: 0.6616 (p0) REVERT: M 169 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7335 (mt-10) REVERT: M 209 MET cc_start: 0.5254 (pp-130) cc_final: 0.4972 (pp-130) REVERT: M 237 GLN cc_start: 0.6689 (pm20) cc_final: 0.6227 (pm20) REVERT: M 285 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: N 23 TYR cc_start: 0.5977 (m-80) cc_final: 0.5461 (m-80) REVERT: N 85 GLU cc_start: 0.8774 (pp20) cc_final: 0.8199 (pp20) REVERT: N 86 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8296 (mmmt) outliers start: 65 outliers final: 46 residues processed: 458 average time/residue: 0.1560 time to fit residues: 97.8967 Evaluate side-chains 481 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 426 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 58 THR 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 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 D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 91 LYS 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 24 LEU 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 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain K residue 165 ARG 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 358 ILE Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 398 LYS 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 172 LEU Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 0.0470 chunk 133 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** K 203 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3917 r_free = 0.3917 target = 0.113189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095599 restraints weight = 54753.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.097848 restraints weight = 30192.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099367 restraints weight = 19865.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.100354 restraints weight = 14871.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100981 restraints weight = 12313.544| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17881 Z= 0.202 Angle : 0.997 17.452 25382 Z= 0.522 Chirality : 0.052 0.258 2864 Planarity : 0.007 0.144 2198 Dihedral : 29.258 172.065 4765 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 5.59 % Allowed : 34.78 % 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: -3.28 (0.21), residues: 1323 helix: -1.57 (0.18), residues: 630 sheet: -2.08 (0.88), residues: 27 loop : -2.83 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 83 TYR 0.040 0.003 TYR C 52 PHE 0.054 0.003 PHE E 67 TRP 0.030 0.002 TRP M 279 HIS 0.006 0.001 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (17881) covalent geometry : angle 0.99670 / 0.52 (25382) hydrogen bonds : bond 0.05862 / 3.81 ( 735) hydrogen bonds : angle 4.55718 / 3.15 ( 1811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3388.96 seconds wall clock time: 59 minutes 6.23 seconds (3546.23 seconds total)