Starting phenix.real_space_refine on Mon Jun 16 06:00:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9v_32373/06_2025/7w9v_32373.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9v_32373/06_2025/7w9v_32373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9v_32373/06_2025/7w9v_32373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9v_32373/06_2025/7w9v_32373.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9v_32373/06_2025/7w9v_32373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9v_32373/06_2025/7w9v_32373.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 47 5.16 5 C 9458 2.51 5 N 3002 2.21 5 O 3615 1.98 5 H 2136 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18546 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1008 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 841 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 996 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 937 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1008 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 785 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1015 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 906 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3246 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3292 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4512 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 514} Chain breaks: 2 Time building chain proxies: 11.34, per 1000 atoms: 0.61 Number of scatterers: 18546 At special positions: 0 Unit cell: (142.31, 116.63, 142.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 288 15.00 O 3615 8.00 N 3002 7.00 C 9458 6.00 H 2136 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K1201 " - pdb=" SG CYS K1204 " distance=2.57 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: 5.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 15 sheets defined 61.3% alpha, 7.8% beta 140 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.864A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.184A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.608A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.656A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.911A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.519A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.654A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.586A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.720A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.602A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.531A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.635A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.506A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.854A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 1050 through 1067 Proline residue: K1060 - end of helix removed outlier: 3.605A pdb=" N LEU K1065 " --> pdb=" O THR K1061 " (cutoff:3.500A) Processing helix chain 'K' and resid 1072 through 1076 Processing helix chain 'K' and resid 1088 through 1093 Processing helix chain 'K' and resid 1098 through 1108 Processing helix chain 'K' and resid 1113 through 1132 removed outlier: 4.028A pdb=" N TYR K1117 " --> pdb=" O GLU K1113 " (cutoff:3.500A) Processing helix chain 'K' and resid 1136 through 1160 removed outlier: 3.653A pdb=" N LYS K1140 " --> pdb=" O SER K1136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1202 through 1208 removed outlier: 3.684A pdb=" N ASN K1206 " --> pdb=" O GLU K1202 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE K1208 " --> pdb=" O CYS K1204 " (cutoff:3.500A) Processing helix chain 'K' and resid 1229 through 1231 No H-bonds generated for 'chain 'K' and resid 1229 through 1231' Processing helix chain 'K' and resid 1256 through 1260 Processing helix chain 'K' and resid 1272 through 1279 removed outlier: 3.681A pdb=" N SER K1279 " --> pdb=" O CYS K1275 " (cutoff:3.500A) Processing helix chain 'K' and resid 1296 through 1314 Processing helix chain 'K' and resid 1336 through 1344 Processing helix chain 'K' and resid 1406 through 1408 No H-bonds generated for 'chain 'K' and resid 1406 through 1408' Processing helix chain 'K' and resid 1409 through 1429 Processing helix chain 'K' and resid 1459 through 1477 Processing helix chain 'K' and resid 1486 through 1493 Processing helix chain 'K' and resid 1497 through 1501 Processing helix chain 'K' and resid 1507 through 1520 removed outlier: 4.016A pdb=" N ASN K1511 " --> pdb=" O ASP K1507 " (cutoff:3.500A) Processing helix chain 'K' and resid 1583 through 1591 Processing helix chain 'K' and resid 1602 through 1608 removed outlier: 3.755A pdb=" N ALA K1605 " --> pdb=" O ALA K1602 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K1608 " --> pdb=" O ALA K1605 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1625 Processing helix chain 'K' and resid 1627 through 1638 Processing helix chain 'K' and resid 1643 through 1661 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.360A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.794A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.694A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.642A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.195A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.634A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 1175 through 1176 removed outlier: 4.486A pdb=" N LEU K1175 " --> pdb=" O ILE K1185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1198 through 1201 Processing sheet with id=AB4, first strand: chain 'K' and resid 1212 through 1215 Processing sheet with id=AB5, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id=AB6, first strand: chain 'K' and resid 1321 through 1334 removed outlier: 7.971A pdb=" N VAL K1321 " --> pdb=" O GLU K1365 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU K1365 " --> pdb=" O VAL K1321 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL K1323 " --> pdb=" O PHE K1363 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE K1363 " --> pdb=" O VAL K1323 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL K1325 " --> pdb=" O PHE K1361 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE K1361 " --> pdb=" O VAL K1325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS K1327 " --> pdb=" O ALA K1359 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR K1381 " --> pdb=" O PRO K1354 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG K1356 " --> pdb=" O GLN K1379 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN K1379 " --> pdb=" O ARG K1356 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS K1358 " --> pdb=" O HIS K1377 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS K1377 " --> pdb=" O LYS K1358 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU K1360 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY K1375 " --> pdb=" O LEU K1360 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA K1362 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE K1373 " --> pdb=" O SER K1400 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER K1400 " --> pdb=" O PHE K1373 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY K1375 " --> pdb=" O LEU K1398 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU K1398 " --> pdb=" O GLY K1375 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 716 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2132 1.13 - 1.31: 2059 1.31 - 1.48: 8429 1.48 - 1.65: 6779 1.65 - 1.83: 70 Bond restraints: 19469 Sorted by residual: bond pdb=" N2 DG I 52 " pdb=" H21 DG I 52 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N2 DG I -40 " pdb=" H21 DG I -40 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NH1 ARG C 42 " pdb="HH12 ARG C 42 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N ILE B 66 " pdb=" H ILE B 66 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE ARG A 40 " pdb=" HE ARG A 40 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 19464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.12: 27428 5.12 - 10.23: 890 10.23 - 15.35: 27 15.35 - 20.46: 9 20.46 - 25.58: 4 Bond angle restraints: 28358 Sorted by residual: angle pdb=" C6 DA J 26 " pdb=" N6 DA J 26 " pdb=" H61 DA J 26 " ideal model delta sigma weight residual 120.00 94.42 25.58 1.50e+00 4.44e-01 2.91e+02 angle pdb=" C6 DA I 46 " pdb=" N6 DA I 46 " pdb=" H61 DA I 46 " ideal model delta sigma weight residual 120.00 97.93 22.07 1.50e+00 4.44e-01 2.17e+02 angle pdb=" C6 DA I -15 " pdb=" N6 DA I -15 " pdb=" H61 DA I -15 " ideal model delta sigma weight residual 120.00 98.53 21.47 1.50e+00 4.44e-01 2.05e+02 angle pdb=" C6 DA I -14 " pdb=" N6 DA I -14 " pdb=" H61 DA I -14 " ideal model delta sigma weight residual 120.00 98.98 21.02 1.50e+00 4.44e-01 1.96e+02 angle pdb=" C6 DA J 6 " pdb=" N6 DA J 6 " pdb=" H61 DA J 6 " ideal model delta sigma weight residual 120.00 99.60 20.40 1.50e+00 4.44e-01 1.85e+02 ... (remaining 28353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 9362 33.24 - 66.47: 1579 66.47 - 99.71: 35 99.71 - 132.95: 1 132.95 - 166.19: 1 Dihedral angle restraints: 10978 sinusoidal: 7168 harmonic: 3810 Sorted by residual: dihedral pdb=" CB CYS K1201 " pdb=" SG CYS K1201 " pdb=" SG CYS K1204 " pdb=" CB CYS K1204 " ideal model delta sinusoidal sigma weight residual 93.00 152.11 -59.11 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CG ARG K1297 " pdb=" CD ARG K1297 " pdb=" NE ARG K1297 " pdb=" CZ ARG K1297 " ideal model delta sinusoidal sigma weight residual -90.00 -10.93 -79.07 2 1.50e+01 4.44e-03 2.06e+01 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N THR D 52 " pdb=" CA THR D 52 " ideal model delta harmonic sigma weight residual 180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 10975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2271 0.055 - 0.110: 339 0.110 - 0.165: 93 0.165 - 0.220: 36 0.220 - 0.275: 8 Chirality restraints: 2747 Sorted by residual: chirality pdb=" CA GLN K1661 " pdb=" N GLN K1661 " pdb=" C GLN K1661 " pdb=" CB GLN K1661 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ALA K1359 " pdb=" N ALA K1359 " pdb=" C ALA K1359 " pdb=" CB ALA K1359 " both_signs ideal model delta sigma weight residual False 2.48 2.73 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL K1401 " pdb=" N VAL K1401 " pdb=" C VAL K1401 " pdb=" CB VAL K1401 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2744 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 49 " -0.050 2.00e-02 2.50e+03 3.09e-02 1.67e+01 pdb=" CG HIS D 49 " 0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS D 49 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS D 49 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS D 49 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS D 49 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 HIS D 49 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K1509 " 0.042 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP K1509 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP K1509 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP K1509 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP K1509 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K1509 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP K1509 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP K1509 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP K1509 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP K1509 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE K1619 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO K1620 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO K1620 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K1620 " 0.038 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.79: 39 1.79 - 2.49: 1764 2.49 - 3.19: 23635 3.19 - 3.90: 50038 3.90 - 4.60: 70621 Nonbonded interactions: 146097 Sorted by model distance: nonbonded pdb="HH12 ARG F 78 " pdb=" HG1 THR F 82 " model vdw 1.082 2.100 nonbonded pdb="HH12 ARG D 86 " pdb=" OE2 GLU D 93 " model vdw 1.221 2.450 nonbonded pdb=" HH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 1.347 2.450 nonbonded pdb="HE21 GLN A 68 " pdb="HH21 ARG A 72 " model vdw 1.350 2.100 nonbonded pdb=" OD2 ASP E 106 " pdb=" HE ARG E 131 " model vdw 1.399 2.450 ... (remaining 146092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 32 through 124) selection = chain 'H' } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 52.590 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 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 0.541 17334 Z= 0.451 Angle : 0.871 17.056 24660 Z= 0.558 Chirality : 0.050 0.275 2747 Planarity : 0.006 0.071 2138 Dihedral : 25.019 166.186 7253 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.44 % Allowed : 4.26 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1280 helix: -0.19 (0.17), residues: 768 sheet: -0.22 (0.62), residues: 64 loop : -0.93 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP K1509 HIS 0.007 0.002 HIS K1402 PHE 0.031 0.004 PHE K1641 TYR 0.036 0.003 TYR K1131 ARG 0.011 0.001 ARG K1305 Details of bonding type rmsd hydrogen bonds : bond 0.11640 ( 948) hydrogen bonds : angle 4.80483 ( 2429) SS BOND : bond 0.54135 ( 1) SS BOND : angle 12.32379 ( 2) covalent geometry : bond 0.00647 (17333) covalent geometry : angle 0.86431 (24658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 329 time to evaluate : 1.367 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 59 GLU cc_start: 0.8367 (pm20) cc_final: 0.8135 (pm20) REVERT: A 93 GLN cc_start: 0.8813 (tt0) cc_final: 0.8610 (tt0) REVERT: A 97 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 107 THR cc_start: 0.9561 (m) cc_final: 0.9217 (p) REVERT: B 79 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8843 (mptt) REVERT: B 84 MET cc_start: 0.8254 (mmm) cc_final: 0.7886 (tpp) REVERT: B 88 TYR cc_start: 0.8766 (m-10) cc_final: 0.8447 (m-80) REVERT: C 20 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8128 (ttm-80) REVERT: C 64 GLU cc_start: 0.8801 (tt0) cc_final: 0.8503 (tm-30) REVERT: C 84 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8909 (tp-100) REVERT: C 104 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8509 (mm-40) REVERT: D 45 LEU cc_start: 0.9145 (tp) cc_final: 0.8854 (tp) REVERT: D 54 ILE cc_start: 0.9542 (tt) cc_final: 0.9280 (mp) REVERT: D 59 MET cc_start: 0.9396 (tpt) cc_final: 0.9152 (tpp) REVERT: F 84 MET cc_start: 0.8857 (mmm) cc_final: 0.8178 (tpp) REVERT: G 27 VAL cc_start: 0.9105 (m) cc_final: 0.8873 (p) REVERT: G 56 GLU cc_start: 0.8542 (tt0) cc_final: 0.8337 (tm-30) REVERT: G 64 GLU cc_start: 0.9047 (tp30) cc_final: 0.8502 (tp30) REVERT: G 84 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8589 (tm-30) REVERT: H 59 MET cc_start: 0.9166 (tpt) cc_final: 0.8812 (tpp) REVERT: H 67 ASN cc_start: 0.8926 (m-40) cc_final: 0.8564 (m-40) REVERT: H 99 ARG cc_start: 0.9157 (mmm-85) cc_final: 0.8779 (mtt-85) REVERT: H 105 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8183 (mm-30) REVERT: K 1088 ASP cc_start: 0.5131 (p0) cc_final: 0.4904 (t0) outliers start: 5 outliers final: 1 residues processed: 333 average time/residue: 0.5002 time to fit residues: 222.3322 Evaluate side-chains 198 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1397 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 0.0570 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN H 63 ASN K1151 GLN K1196 ASN K1256 GLN K1402 HIS ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1481 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.099993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060963 restraints weight = 85734.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062190 restraints weight = 45430.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062876 restraints weight = 32093.943| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17334 Z= 0.147 Angle : 0.504 5.892 24660 Z= 0.300 Chirality : 0.032 0.140 2747 Planarity : 0.004 0.038 2138 Dihedral : 28.105 167.219 4617 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.22 % Allowed : 12.08 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1280 helix: 1.70 (0.19), residues: 772 sheet: 0.32 (0.61), residues: 68 loop : -0.24 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K1466 HIS 0.010 0.001 HIS C 31 PHE 0.014 0.001 PHE K1504 TYR 0.015 0.001 TYR K1089 ARG 0.003 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 948) hydrogen bonds : angle 3.61447 ( 2429) SS BOND : bond 0.00392 ( 1) SS BOND : angle 2.08664 ( 2) covalent geometry : bond 0.00297 (17333) covalent geometry : angle 0.50328 (24658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8035 (tt0) REVERT: B 88 TYR cc_start: 0.8510 (m-10) cc_final: 0.8195 (m-80) REVERT: C 38 ASN cc_start: 0.8260 (t0) cc_final: 0.7974 (t0) REVERT: C 84 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8978 (tp-100) REVERT: D 45 LEU cc_start: 0.9325 (tp) cc_final: 0.8857 (tp) REVERT: D 54 ILE cc_start: 0.9447 (tt) cc_final: 0.9199 (mp) REVERT: E 56 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8624 (mtpt) REVERT: E 120 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5764 (mtt) REVERT: F 47 SER cc_start: 0.9192 (t) cc_final: 0.8919 (t) REVERT: F 88 TYR cc_start: 0.8872 (m-80) cc_final: 0.8670 (m-80) REVERT: G 36 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8959 (mmtt) REVERT: G 38 ASN cc_start: 0.8461 (t0) cc_final: 0.8074 (t0) REVERT: G 64 GLU cc_start: 0.8643 (tp30) cc_final: 0.8350 (tm-30) REVERT: H 63 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.8939 (t0) REVERT: H 67 ASN cc_start: 0.8905 (m-40) cc_final: 0.8491 (m-40) REVERT: K 1088 ASP cc_start: 0.5647 (p0) cc_final: 0.5107 (t0) REVERT: K 1381 TYR cc_start: -0.0802 (m-80) cc_final: -0.1105 (m-80) outliers start: 25 outliers final: 18 residues processed: 236 average time/residue: 0.3495 time to fit residues: 121.9968 Evaluate side-chains 204 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain K residue 1196 ASN Chi-restraints excluded: chain K residue 1435 ILE Chi-restraints excluded: chain K residue 1486 ILE Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain K residue 1624 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 113 optimal weight: 40.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.099779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060793 restraints weight = 86032.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061986 restraints weight = 47103.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062590 restraints weight = 33487.435| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17334 Z= 0.135 Angle : 0.469 6.378 24660 Z= 0.281 Chirality : 0.031 0.131 2747 Planarity : 0.003 0.030 2138 Dihedral : 27.949 167.077 4615 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 25.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.87 % Allowed : 14.30 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.24), residues: 1280 helix: 2.34 (0.19), residues: 773 sheet: 0.30 (0.61), residues: 68 loop : 0.00 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K1466 HIS 0.006 0.001 HIS C 31 PHE 0.022 0.001 PHE K1403 TYR 0.016 0.001 TYR K1131 ARG 0.003 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 948) hydrogen bonds : angle 3.26234 ( 2429) SS BOND : bond 0.00480 ( 1) SS BOND : angle 1.83953 ( 2) covalent geometry : bond 0.00281 (17333) covalent geometry : angle 0.46845 (24658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.385 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: A 59 GLU cc_start: 0.8330 (pm20) cc_final: 0.8080 (pm20) REVERT: E 56 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8647 (mtpt) REVERT: E 120 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.6051 (mtt) REVERT: F 47 SER cc_start: 0.9208 (t) cc_final: 0.8747 (m) REVERT: F 88 TYR cc_start: 0.9004 (m-80) cc_final: 0.8758 (m-80) REVERT: G 36 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8933 (mmtt) REVERT: G 38 ASN cc_start: 0.8455 (t0) cc_final: 0.8202 (t0) REVERT: G 64 GLU cc_start: 0.8529 (tp30) cc_final: 0.8302 (tm-30) REVERT: G 84 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8238 (tp-100) REVERT: H 67 ASN cc_start: 0.8960 (m-40) cc_final: 0.8643 (m-40) REVERT: K 1088 ASP cc_start: 0.5702 (p0) cc_final: 0.5280 (t0) outliers start: 21 outliers final: 14 residues processed: 194 average time/residue: 0.3442 time to fit residues: 99.8475 Evaluate side-chains 193 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 1486 ILE Chi-restraints excluded: chain K residue 1600 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1151 GLN K1261 HIS ** K1415 HIS ** 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 = 0.3787 r_free = 0.3787 target = 0.094542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054998 restraints weight = 88351.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056052 restraints weight = 49381.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.056647 restraints weight = 35882.174| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 17334 Z= 0.301 Angle : 0.643 11.771 24660 Z= 0.360 Chirality : 0.038 0.163 2747 Planarity : 0.004 0.031 2138 Dihedral : 28.459 173.441 4615 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 36.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.20 % Allowed : 16.52 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1280 helix: 1.92 (0.18), residues: 771 sheet: 0.09 (0.58), residues: 78 loop : -0.10 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K1466 HIS 0.007 0.002 HIS F 75 PHE 0.020 0.002 PHE K1403 TYR 0.026 0.002 TYR B 88 ARG 0.008 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.05767 ( 948) hydrogen bonds : angle 4.03677 ( 2429) SS BOND : bond 0.00309 ( 1) SS BOND : angle 1.37177 ( 2) covalent geometry : bond 0.00670 (17333) covalent geometry : angle 0.64295 (24658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 88 TYR cc_start: 0.8448 (m-80) cc_final: 0.7734 (m-80) REVERT: D 42 TYR cc_start: 0.8246 (t80) cc_final: 0.7561 (t80) REVERT: D 83 TYR cc_start: 0.8122 (m-10) cc_final: 0.7518 (m-10) REVERT: F 88 TYR cc_start: 0.9099 (m-80) cc_final: 0.8824 (m-80) REVERT: G 36 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8930 (mmtt) REVERT: G 38 ASN cc_start: 0.8443 (t0) cc_final: 0.8037 (t0) REVERT: G 64 GLU cc_start: 0.8580 (tp30) cc_final: 0.8374 (tm-30) REVERT: K 1088 ASP cc_start: 0.5303 (p0) cc_final: 0.4824 (t0) REVERT: K 1327 HIS cc_start: 0.2209 (t70) cc_final: 0.1824 (t-170) outliers start: 36 outliers final: 28 residues processed: 196 average time/residue: 0.3303 time to fit residues: 97.2209 Evaluate side-chains 190 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 1083 LEU Chi-restraints excluded: chain K residue 1486 ILE Chi-restraints excluded: chain K residue 1600 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 50.0000 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.096794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057198 restraints weight = 87679.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058298 restraints weight = 48151.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058930 restraints weight = 35131.462| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17334 Z= 0.139 Angle : 0.474 6.351 24660 Z= 0.283 Chirality : 0.031 0.136 2747 Planarity : 0.003 0.026 2138 Dihedral : 28.190 169.069 4615 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.51 % Allowed : 18.21 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.24), residues: 1280 helix: 2.61 (0.19), residues: 771 sheet: 0.08 (0.57), residues: 78 loop : 0.08 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K1466 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.001 PHE K1403 TYR 0.015 0.001 TYR K1131 ARG 0.004 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 948) hydrogen bonds : angle 3.28073 ( 2429) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.93851 ( 2) covalent geometry : bond 0.00291 (17333) covalent geometry : angle 0.47367 (24658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.559 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: A 93 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 88 TYR cc_start: 0.8322 (m-80) cc_final: 0.8089 (m-80) REVERT: D 42 TYR cc_start: 0.7955 (t80) cc_final: 0.7310 (t80) REVERT: F 88 TYR cc_start: 0.9049 (m-10) cc_final: 0.8745 (m-80) REVERT: G 36 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8931 (mmtt) REVERT: H 63 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8924 (t0) REVERT: K 1088 ASP cc_start: 0.5508 (p0) cc_final: 0.5091 (t0) REVERT: K 1137 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.4537 (pmt170) REVERT: K 1327 HIS cc_start: 0.2275 (t70) cc_final: 0.1513 (t-170) outliers start: 17 outliers final: 10 residues processed: 186 average time/residue: 0.3353 time to fit residues: 94.1147 Evaluate side-chains 179 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 1137 ARG Chi-restraints excluded: chain K residue 1486 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 113 optimal weight: 0.1980 chunk 134 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.096242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056797 restraints weight = 88118.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.057845 restraints weight = 49344.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058427 restraints weight = 35520.953| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17334 Z= 0.165 Angle : 0.477 6.978 24660 Z= 0.284 Chirality : 0.031 0.141 2747 Planarity : 0.003 0.026 2138 Dihedral : 28.173 171.938 4615 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 32.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.04 % Allowed : 17.94 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.24), residues: 1280 helix: 2.70 (0.19), residues: 771 sheet: 0.11 (0.57), residues: 78 loop : 0.14 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K1466 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE K1403 TYR 0.015 0.001 TYR K1131 ARG 0.003 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 948) hydrogen bonds : angle 3.28037 ( 2429) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.88797 ( 2) covalent geometry : bond 0.00357 (17333) covalent geometry : angle 0.47701 (24658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.423 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: A 59 GLU cc_start: 0.8280 (pm20) cc_final: 0.8079 (pm20) REVERT: A 93 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8231 (tm-30) REVERT: B 88 TYR cc_start: 0.8391 (m-10) cc_final: 0.7453 (m-80) REVERT: D 45 LEU cc_start: 0.9526 (tp) cc_final: 0.9317 (tp) REVERT: D 76 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8672 (mm-30) REVERT: D 83 TYR cc_start: 0.8164 (m-10) cc_final: 0.7486 (m-10) REVERT: D 92 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8525 (mtm-85) REVERT: F 88 TYR cc_start: 0.9086 (m-10) cc_final: 0.8798 (m-80) REVERT: G 36 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8948 (mmtt) REVERT: H 34 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8648 (mtpp) REVERT: K 1088 ASP cc_start: 0.5758 (p0) cc_final: 0.5211 (t0) REVERT: K 1137 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.4609 (pmt170) REVERT: K 1327 HIS cc_start: 0.2168 (t70) cc_final: 0.1764 (t-170) REVERT: K 1339 MET cc_start: -0.5544 (ttm) cc_final: -0.6188 (mmt) outliers start: 23 outliers final: 15 residues processed: 185 average time/residue: 0.3378 time to fit residues: 92.0624 Evaluate side-chains 179 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 1137 ARG Chi-restraints excluded: chain K residue 1486 ILE Chi-restraints excluded: chain K residue 1618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.097517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058258 restraints weight = 87149.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059375 restraints weight = 48294.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059974 restraints weight = 34516.837| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17334 Z= 0.124 Angle : 0.451 9.139 24660 Z= 0.270 Chirality : 0.030 0.137 2747 Planarity : 0.002 0.025 2138 Dihedral : 27.967 169.450 4615 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 30.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.62 % Allowed : 19.18 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.24), residues: 1280 helix: 3.03 (0.19), residues: 770 sheet: 0.09 (0.57), residues: 78 loop : 0.25 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1466 HIS 0.004 0.000 HIS F 75 PHE 0.013 0.001 PHE K1487 TYR 0.012 0.001 TYR K1131 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 948) hydrogen bonds : angle 2.97973 ( 2429) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.81772 ( 2) covalent geometry : bond 0.00259 (17333) covalent geometry : angle 0.45118 (24658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 1.626 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: B 88 TYR cc_start: 0.8275 (m-10) cc_final: 0.8040 (m-80) REVERT: C 84 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8972 (tp-100) REVERT: G 36 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8958 (mmtt) REVERT: H 34 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8687 (mtpt) REVERT: K 1088 ASP cc_start: 0.5870 (p0) cc_final: 0.5456 (t0) REVERT: K 1327 HIS cc_start: 0.2240 (t70) cc_final: 0.1846 (t-170) REVERT: K 1339 MET cc_start: -0.4658 (ttm) cc_final: -0.5653 (mmt) outliers start: 7 outliers final: 4 residues processed: 175 average time/residue: 0.3363 time to fit residues: 87.9034 Evaluate side-chains 168 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 1486 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 30.0000 chunk 151 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.097569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.058112 restraints weight = 87821.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059305 restraints weight = 48502.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059978 restraints weight = 34745.428| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17334 Z= 0.128 Angle : 0.446 5.414 24660 Z= 0.267 Chirality : 0.030 0.136 2747 Planarity : 0.002 0.025 2138 Dihedral : 27.936 171.678 4615 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.62 % Allowed : 19.18 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.25), residues: 1280 helix: 3.15 (0.19), residues: 772 sheet: 0.20 (0.57), residues: 78 loop : 0.30 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1466 HIS 0.004 0.001 HIS F 75 PHE 0.013 0.001 PHE K1403 TYR 0.014 0.001 TYR F 88 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 948) hydrogen bonds : angle 2.91793 ( 2429) SS BOND : bond 0.00237 ( 1) SS BOND : angle 0.81594 ( 2) covalent geometry : bond 0.00270 (17333) covalent geometry : angle 0.44622 (24658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 1.581 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: B 88 TYR cc_start: 0.8252 (m-10) cc_final: 0.7996 (m-80) REVERT: C 84 GLN cc_start: 0.9263 (tp-100) cc_final: 0.9017 (tp-100) REVERT: C 91 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7595 (tm-30) REVERT: D 92 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8531 (mtm-85) REVERT: G 36 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8956 (mmtt) REVERT: H 34 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8690 (mtpt) REVERT: K 1088 ASP cc_start: 0.5846 (p0) cc_final: 0.5434 (t0) REVERT: K 1339 MET cc_start: -0.4647 (ttm) cc_final: -0.5658 (mmt) outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.3512 time to fit residues: 90.0562 Evaluate side-chains 166 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 1486 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 144 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 103 optimal weight: 0.0980 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.094551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055814 restraints weight = 88880.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056204 restraints weight = 50971.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056778 restraints weight = 37764.346| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17334 Z= 0.286 Angle : 0.598 9.768 24660 Z= 0.338 Chirality : 0.036 0.148 2747 Planarity : 0.004 0.030 2138 Dihedral : 28.320 173.136 4615 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 38.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.31 % Allowed : 18.21 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1280 helix: 2.41 (0.18), residues: 775 sheet: -0.06 (0.58), residues: 80 loop : -0.04 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K1466 HIS 0.008 0.001 HIS F 75 PHE 0.013 0.001 PHE K1403 TYR 0.018 0.002 TYR K1131 ARG 0.005 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 948) hydrogen bonds : angle 3.68925 ( 2429) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.97632 ( 2) covalent geometry : bond 0.00632 (17333) covalent geometry : angle 0.59811 (24658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8486 (m-10) cc_final: 0.7760 (m-80) REVERT: D 83 TYR cc_start: 0.8139 (m-10) cc_final: 0.7392 (m-10) REVERT: D 92 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8589 (mtm-85) REVERT: G 36 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8981 (mmtt) REVERT: H 34 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8809 (mtpt) REVERT: K 1088 ASP cc_start: 0.5702 (p0) cc_final: 0.5290 (t0) REVERT: K 1339 MET cc_start: -0.5762 (ttm) cc_final: -0.6499 (mmt) outliers start: 26 outliers final: 19 residues processed: 168 average time/residue: 0.3684 time to fit residues: 92.7634 Evaluate side-chains 165 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 1327 HIS Chi-restraints excluded: chain K residue 1486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.0040 chunk 148 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.095802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057085 restraints weight = 87452.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057713 restraints weight = 50131.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058241 restraints weight = 36864.466| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17334 Z= 0.167 Angle : 0.496 6.061 24660 Z= 0.292 Chirality : 0.032 0.144 2747 Planarity : 0.003 0.026 2138 Dihedral : 28.226 171.425 4615 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 36.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.24 % Allowed : 19.72 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1280 helix: 2.68 (0.19), residues: 778 sheet: 0.01 (0.58), residues: 80 loop : 0.09 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K1466 HIS 0.007 0.001 HIS K1415 PHE 0.011 0.001 PHE K1231 TYR 0.023 0.001 TYR H 83 ARG 0.006 0.000 ARG K1391 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 948) hydrogen bonds : angle 3.27498 ( 2429) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.82573 ( 2) covalent geometry : bond 0.00362 (17333) covalent geometry : angle 0.49552 (24658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ALA 75 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 88 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue MET 90 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue VAL 101 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue ALA 33 is missing expected H atoms. Skipping. Residue ILE 34 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue MET 84 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue ALA 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue ALA 45 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue ALA 66 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue ILE 79 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 86 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue LEU 97 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 101 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ALA 103 is missing expected H atoms. Skipping. Residue VAL 107 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 111 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue VAL 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue ALA 77 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue ALA 81 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8409 (m-10) cc_final: 0.7560 (m-80) REVERT: C 84 GLN cc_start: 0.9255 (tp-100) cc_final: 0.9004 (tp-100) REVERT: D 76 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8649 (mm-30) REVERT: D 83 TYR cc_start: 0.8081 (m-10) cc_final: 0.7318 (m-10) REVERT: D 92 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8535 (mtm-85) REVERT: G 36 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8974 (mmtt) REVERT: H 34 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8731 (mtpt) REVERT: H 59 MET cc_start: 0.9050 (tpp) cc_final: 0.8521 (tpp) REVERT: K 1339 MET cc_start: -0.5710 (ttm) cc_final: -0.6440 (mmt) outliers start: 14 outliers final: 13 residues processed: 171 average time/residue: 0.3320 time to fit residues: 85.9812 Evaluate side-chains 172 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 1327 HIS Chi-restraints excluded: chain K residue 1486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 64 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 119 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.096676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057954 restraints weight = 87606.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058541 restraints weight = 48815.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059182 restraints weight = 35405.512| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17334 Z= 0.137 Angle : 0.464 6.870 24660 Z= 0.275 Chirality : 0.030 0.160 2747 Planarity : 0.003 0.037 2138 Dihedral : 28.063 172.242 4615 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.07 % Allowed : 19.98 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.24), residues: 1280 helix: 2.97 (0.19), residues: 778 sheet: 0.14 (0.64), residues: 70 loop : 0.12 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1466 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE K1231 TYR 0.013 0.001 TYR K1131 ARG 0.003 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 948) hydrogen bonds : angle 3.01591 ( 2429) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.77549 ( 2) covalent geometry : bond 0.00292 (17333) covalent geometry : angle 0.46436 (24658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7222.54 seconds wall clock time: 125 minutes 12.48 seconds (7512.48 seconds total)