Starting phenix.real_space_refine on Wed Apr 10 04:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9v_32373/04_2024/7w9v_32373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9v_32373/04_2024/7w9v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9v_32373/04_2024/7w9v_32373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9v_32373/04_2024/7w9v_32373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9v_32373/04_2024/7w9v_32373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9v_32373/04_2024/7w9v_32373.pdb" } 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 Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1063": "OE1" <-> "OE2" Residue "K GLU 1150": "OE1" <-> "OE2" Residue "K GLU 1263": "OE1" <-> "OE2" Residue "K GLU 1285": "OE1" <-> "OE2" Residue "K TYR 1355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1365": "OE1" <-> "OE2" Residue "K PHE 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1442": "OE1" <-> "OE2" Residue "K GLU 1505": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.73, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 11.72 Conformation dependent library (CDL) restraints added in 2.1 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: 7.82 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: 10.41 Time building geometry restraints manager: 12.08 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: 94.42 - 102.52: 346 102.52 - 110.62: 7486 110.62 - 118.71: 8291 118.71 - 126.81: 11318 126.81 - 134.90: 917 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 1.850 nonbonded pdb=" HH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 1.347 1.850 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 1.850 ... (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 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: 0.810 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: 0.320 Extract box with map and model: 4.040 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 62.740 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.170 ------------------------------------------------------------------------------- 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 : 0.006 0.053 17333 Z= 0.399 Angle : 0.864 9.905 24658 Z= 0.555 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 329 time to evaluate : 1.594 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: 0.5153 time to fit residues: 227.7320 Evaluate side-chains 198 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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: 0.9980 chunk 116 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 C 24 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1481 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17333 Z= 0.168 Angle : 0.500 5.914 24658 Z= 0.298 Chirality : 0.032 0.140 2747 Planarity : 0.004 0.039 2138 Dihedral : 28.078 167.386 4617 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.22 % Allowed : 12.17 % Favored : 85.61 % 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: 1.45 (0.23), residues: 1280 helix: 1.73 (0.19), residues: 771 sheet: 0.32 (0.61), residues: 68 loop : -0.24 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K1466 HIS 0.011 0.001 HIS C 31 PHE 0.014 0.001 PHE K1504 TYR 0.014 0.001 TYR K1089 ARG 0.003 0.000 ARG F 35 *********************** 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 247 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.641 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: A 58 THR cc_start: 0.9451 (p) cc_final: 0.9217 (p) REVERT: A 59 GLU cc_start: 0.8277 (pm20) cc_final: 0.8073 (pm20) REVERT: A 97 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 107 THR cc_start: 0.9454 (m) cc_final: 0.9189 (p) REVERT: A 108 ASN cc_start: 0.9266 (t0) cc_final: 0.9048 (t0) REVERT: A 133 GLU cc_start: 0.7308 (tt0) cc_final: 0.7041 (tt0) REVERT: B 84 MET cc_start: 0.8366 (mmm) cc_final: 0.8062 (tpp) REVERT: B 88 TYR cc_start: 0.8620 (m-10) cc_final: 0.8289 (m-80) REVERT: C 20 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8154 (ttm-80) REVERT: C 38 ASN cc_start: 0.8490 (t0) cc_final: 0.8032 (t0) REVERT: C 64 GLU cc_start: 0.8807 (tt0) cc_final: 0.8476 (tm-30) REVERT: C 104 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8369 (mm-40) REVERT: D 45 LEU cc_start: 0.9126 (tp) cc_final: 0.8811 (tp) REVERT: D 54 ILE cc_start: 0.9518 (tt) cc_final: 0.9242 (mp) REVERT: E 120 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.5460 (mtt) REVERT: F 88 TYR cc_start: 0.9001 (m-80) cc_final: 0.8752 (m-80) REVERT: G 38 ASN cc_start: 0.8424 (t0) cc_final: 0.8041 (t0) REVERT: G 56 GLU cc_start: 0.8606 (tt0) cc_final: 0.8308 (tm-30) REVERT: G 64 GLU cc_start: 0.9057 (tp30) cc_final: 0.8381 (tm-30) REVERT: G 90 ASP cc_start: 0.8915 (t0) cc_final: 0.8620 (t0) REVERT: H 63 ASN cc_start: 0.9457 (OUTLIER) cc_final: 0.9162 (t0) REVERT: H 67 ASN cc_start: 0.8953 (m-40) cc_final: 0.8443 (m-40) REVERT: H 99 ARG cc_start: 0.9115 (mmm-85) cc_final: 0.8865 (mtp85) REVERT: K 1137 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.5117 (pmt170) outliers start: 25 outliers final: 18 residues processed: 232 average time/residue: 0.3550 time to fit residues: 121.3133 Evaluate side-chains 205 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 1137 ARG 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 77 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 0.2980 chunk 112 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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** D 95 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1196 ASN K1256 GLN K1261 HIS ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 17333 Z= 0.409 Angle : 0.654 10.833 24658 Z= 0.366 Chirality : 0.038 0.160 2747 Planarity : 0.004 0.041 2138 Dihedral : 28.393 172.692 4615 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 35.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.46 % Allowed : 15.19 % Favored : 81.35 % 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: 1.71 (0.18), residues: 771 sheet: -0.07 (0.56), residues: 78 loop : -0.19 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1466 HIS 0.012 0.002 HIS K1402 PHE 0.027 0.002 PHE K1403 TYR 0.021 0.002 TYR K1131 ARG 0.007 0.001 ARG A 128 *********************** 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 fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8356 (pm20) cc_final: 0.8094 (pm20) REVERT: A 133 GLU cc_start: 0.7887 (tt0) cc_final: 0.7656 (tt0) REVERT: B 84 MET cc_start: 0.8571 (mmm) cc_final: 0.7985 (tpp) REVERT: B 88 TYR cc_start: 0.8679 (m-10) cc_final: 0.8303 (m-80) REVERT: C 20 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8320 (ttm-80) REVERT: C 38 ASN cc_start: 0.8560 (t0) cc_final: 0.8303 (t0) REVERT: C 64 GLU cc_start: 0.8841 (tt0) cc_final: 0.8561 (tm-30) REVERT: C 104 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8552 (mm-40) REVERT: F 88 TYR cc_start: 0.9029 (m-80) cc_final: 0.8812 (m-80) REVERT: G 38 ASN cc_start: 0.8498 (t0) cc_final: 0.8261 (t0) REVERT: G 56 GLU cc_start: 0.8806 (tt0) cc_final: 0.8462 (tm-30) REVERT: G 64 GLU cc_start: 0.9072 (tp30) cc_final: 0.8427 (tm-30) REVERT: G 90 ASP cc_start: 0.9045 (t0) cc_final: 0.8828 (t0) REVERT: H 67 ASN cc_start: 0.9117 (m-40) cc_final: 0.8696 (m-40) REVERT: H 99 ARG cc_start: 0.9152 (mmm-85) cc_final: 0.8746 (mtp85) REVERT: K 1092 ILE cc_start: 0.3027 (mm) cc_final: 0.2752 (mm) REVERT: K 1137 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5035 (pmt170) REVERT: K 1339 MET cc_start: -0.2534 (mmt) cc_final: -0.4446 (ttt) outliers start: 39 outliers final: 30 residues processed: 193 average time/residue: 0.3610 time to fit residues: 103.3409 Evaluate side-chains 192 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 77 LYS 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 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 E residue 130 ILE Chi-restraints excluded: chain F residue 46 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 1137 ARG Chi-restraints excluded: chain K residue 1188 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 8.9990 chunk 105 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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** K1151 GLN ** K1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 17333 Z= 0.386 Angle : 0.607 8.752 24658 Z= 0.348 Chirality : 0.037 0.143 2747 Planarity : 0.004 0.031 2138 Dihedral : 28.499 171.519 4615 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 39.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.35 % Allowed : 16.16 % 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: 1.38 (0.23), residues: 1280 helix: 1.75 (0.18), residues: 768 sheet: -0.22 (0.58), residues: 78 loop : -0.32 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K1466 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.002 PHE K1403 TYR 0.021 0.002 TYR K1131 ARG 0.006 0.000 ARG A 128 *********************** 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 212 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7936 (tt0) cc_final: 0.7642 (tt0) REVERT: B 73 THR cc_start: 0.9644 (OUTLIER) cc_final: 0.9363 (p) REVERT: B 88 TYR cc_start: 0.8729 (m-10) cc_final: 0.8511 (m-80) REVERT: C 20 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8313 (ttm-80) REVERT: C 38 ASN cc_start: 0.8647 (t0) cc_final: 0.8427 (t0) REVERT: C 64 GLU cc_start: 0.8787 (tt0) cc_final: 0.8470 (tm-30) REVERT: C 104 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8559 (mm-40) REVERT: F 88 TYR cc_start: 0.9070 (m-10) cc_final: 0.8792 (m-80) REVERT: G 38 ASN cc_start: 0.8584 (t0) cc_final: 0.8349 (t0) REVERT: G 56 GLU cc_start: 0.8751 (tt0) cc_final: 0.8450 (tm-30) REVERT: G 64 GLU cc_start: 0.9000 (tp30) cc_final: 0.8480 (tm-30) REVERT: H 99 ARG cc_start: 0.9158 (mmm-85) cc_final: 0.8753 (mtp85) REVERT: K 1092 ILE cc_start: 0.3198 (mm) cc_final: 0.2903 (mm) REVERT: K 1137 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.5015 (pmt170) REVERT: K 1339 MET cc_start: -0.2426 (mmt) cc_final: -0.4406 (ttt) REVERT: K 1470 MET cc_start: 0.0483 (ppp) cc_final: -0.0329 (ppp) outliers start: 49 outliers final: 37 residues processed: 199 average time/residue: 0.3471 time to fit residues: 102.9000 Evaluate side-chains 189 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 89 VAL 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 62 LEU Chi-restraints excluded: chain B residue 73 THR 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 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 80 LEU 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 E residue 120 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1137 ARG Chi-restraints excluded: chain K residue 1188 ASP Chi-restraints excluded: chain K residue 1418 LEU Chi-restraints excluded: chain K residue 1486 ILE Chi-restraints excluded: chain K residue 1618 LEU Chi-restraints excluded: chain K residue 1624 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 40.0000 chunk 102 optimal weight: 0.0040 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- 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** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17333 Z= 0.324 Angle : 0.559 6.638 24658 Z= 0.324 Chirality : 0.035 0.150 2747 Planarity : 0.003 0.032 2138 Dihedral : 28.546 174.338 4615 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 39.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.17 % Allowed : 18.21 % Favored : 77.62 % 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: 1.55 (0.24), residues: 1280 helix: 1.91 (0.19), residues: 776 sheet: -0.05 (0.59), residues: 78 loop : -0.36 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1466 HIS 0.008 0.001 HIS K1402 PHE 0.023 0.001 PHE K1403 TYR 0.018 0.001 TYR K1131 ARG 0.003 0.000 ARG B 40 *********************** 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 202 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 155 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9345 (p) REVERT: C 20 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8279 (ttm-80) REVERT: C 64 GLU cc_start: 0.8777 (tt0) cc_final: 0.8456 (tm-30) REVERT: E 122 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8905 (pttp) REVERT: F 88 TYR cc_start: 0.9067 (m-10) cc_final: 0.8824 (m-80) REVERT: G 38 ASN cc_start: 0.8629 (t0) cc_final: 0.8351 (t0) REVERT: G 56 GLU cc_start: 0.8720 (tt0) cc_final: 0.8356 (tm-30) REVERT: G 64 GLU cc_start: 0.8955 (tp30) cc_final: 0.8458 (tm-30) REVERT: H 34 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8490 (mtpp) REVERT: H 99 ARG cc_start: 0.9134 (mmm-85) cc_final: 0.8739 (mtp85) REVERT: K 1092 ILE cc_start: 0.3496 (mm) cc_final: 0.3104 (mm) REVERT: K 1137 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.5008 (pmt170) REVERT: K 1339 MET cc_start: -0.2197 (mmt) cc_final: -0.4255 (ttt) REVERT: K 1470 MET cc_start: 0.0748 (ppp) cc_final: 0.0084 (ppp) outliers start: 47 outliers final: 34 residues processed: 191 average time/residue: 0.3489 time to fit residues: 99.4319 Evaluate side-chains 184 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 A residue 107 THR 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 73 THR 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 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1137 ARG Chi-restraints excluded: chain K residue 1486 ILE Chi-restraints excluded: chain K residue 1600 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 0.0870 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17333 Z= 0.141 Angle : 0.467 7.481 24658 Z= 0.280 Chirality : 0.031 0.141 2747 Planarity : 0.003 0.029 2138 Dihedral : 28.277 169.861 4615 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 33.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.42 % Allowed : 21.14 % Favored : 77.44 % 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: 2.30 (0.24), residues: 1280 helix: 2.55 (0.19), residues: 776 sheet: 0.10 (0.64), residues: 68 loop : -0.11 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1466 HIS 0.004 0.000 HIS F 75 PHE 0.016 0.001 PHE K1403 TYR 0.015 0.001 TYR B 88 ARG 0.004 0.000 ARG A 49 *********************** 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 184 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8290 (mm-30) REVERT: A 133 GLU cc_start: 0.7426 (tt0) cc_final: 0.7219 (tt0) REVERT: C 20 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: C 64 GLU cc_start: 0.8767 (tt0) cc_final: 0.8436 (tm-30) REVERT: C 91 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 42 TYR cc_start: 0.7771 (t80) cc_final: 0.7167 (t80) REVERT: D 76 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8740 (mm-30) REVERT: D 92 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8756 (mtm-85) REVERT: F 88 TYR cc_start: 0.9018 (m-10) cc_final: 0.8812 (m-80) REVERT: G 56 GLU cc_start: 0.8556 (tt0) cc_final: 0.8150 (tm-30) REVERT: G 64 GLU cc_start: 0.8936 (tp30) cc_final: 0.8409 (tm-30) REVERT: H 34 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8359 (mtpt) REVERT: H 99 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8821 (mtp85) REVERT: K 1092 ILE cc_start: 0.3291 (mm) cc_final: 0.2945 (mm) REVERT: K 1137 ARG cc_start: 0.5538 (OUTLIER) cc_final: 0.5298 (pmt170) REVERT: K 1339 MET cc_start: -0.2124 (mmt) cc_final: -0.4176 (ttt) REVERT: K 1470 MET cc_start: 0.0708 (ppp) cc_final: 0.0021 (ppp) outliers start: 16 outliers final: 9 residues processed: 179 average time/residue: 0.3553 time to fit residues: 94.0637 Evaluate side-chains 167 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 1137 ARG Chi-restraints excluded: chain K residue 1486 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17333 Z= 0.352 Angle : 0.570 8.721 24658 Z= 0.327 Chirality : 0.035 0.151 2747 Planarity : 0.003 0.032 2138 Dihedral : 28.547 174.584 4615 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 42.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.58 % Allowed : 20.25 % Favored : 77.18 % 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: 1.87 (0.24), residues: 1280 helix: 2.20 (0.19), residues: 776 sheet: -0.08 (0.61), residues: 80 loop : -0.28 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K1466 HIS 0.006 0.001 HIS F 75 PHE 0.016 0.001 PHE K1403 TYR 0.031 0.002 TYR B 88 ARG 0.003 0.000 ARG F 45 *********************** 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 173 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 73 THR cc_start: 0.9650 (OUTLIER) cc_final: 0.9387 (p) REVERT: B 88 TYR cc_start: 0.8613 (m-80) cc_final: 0.7776 (m-10) REVERT: C 20 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8297 (ttm-80) REVERT: C 64 GLU cc_start: 0.8783 (tt0) cc_final: 0.8476 (tm-30) REVERT: C 91 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8138 (tm-30) REVERT: D 35 GLU cc_start: 0.7652 (pp20) cc_final: 0.7402 (pp20) REVERT: D 76 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8806 (mm-30) REVERT: D 92 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8756 (mtm-85) REVERT: F 88 TYR cc_start: 0.9065 (m-10) cc_final: 0.8815 (m-80) REVERT: G 56 GLU cc_start: 0.8751 (tt0) cc_final: 0.8374 (tm-30) REVERT: G 64 GLU cc_start: 0.8939 (tp30) cc_final: 0.8451 (tm-30) REVERT: H 34 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8495 (mtpt) REVERT: H 99 ARG cc_start: 0.9140 (mmm-85) cc_final: 0.8818 (mtp85) REVERT: K 1137 ARG cc_start: 0.5556 (OUTLIER) cc_final: 0.5075 (pmt170) REVERT: K 1339 MET cc_start: -0.2238 (mmt) cc_final: -0.4256 (ttt) REVERT: K 1470 MET cc_start: 0.0710 (ppp) cc_final: 0.0047 (ppp) outliers start: 29 outliers final: 21 residues processed: 163 average time/residue: 0.3686 time to fit residues: 88.0537 Evaluate side-chains 165 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 1098 ASP Chi-restraints excluded: chain K residue 1137 ARG 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 59 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** B 93 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17333 Z= 0.213 Angle : 0.488 6.534 24658 Z= 0.289 Chirality : 0.032 0.145 2747 Planarity : 0.003 0.030 2138 Dihedral : 28.431 171.534 4615 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 39.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.31 % Allowed : 20.69 % Favored : 77.00 % 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: 2.14 (0.24), residues: 1280 helix: 2.45 (0.19), residues: 776 sheet: -0.16 (0.66), residues: 70 loop : -0.20 (0.30), residues: 434 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 0.044 0.001 TYR B 88 ARG 0.002 0.000 ARG B 40 *********************** 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 177 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 73 THR cc_start: 0.9632 (OUTLIER) cc_final: 0.9351 (p) REVERT: B 88 TYR cc_start: 0.8459 (m-80) cc_final: 0.7730 (m-10) REVERT: C 64 GLU cc_start: 0.8790 (tt0) cc_final: 0.8495 (tm-30) REVERT: D 35 GLU cc_start: 0.7601 (pp20) cc_final: 0.7375 (pp20) REVERT: D 76 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8829 (mm-30) REVERT: D 92 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8738 (mtm-85) REVERT: E 122 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8704 (tptp) REVERT: G 56 GLU cc_start: 0.8687 (tt0) cc_final: 0.8216 (tm-30) REVERT: G 64 GLU cc_start: 0.8916 (tp30) cc_final: 0.8426 (tm-30) REVERT: H 34 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8437 (mtpt) REVERT: H 59 MET cc_start: 0.9057 (tpp) cc_final: 0.8652 (tpp) REVERT: H 99 ARG cc_start: 0.9121 (mmm-85) cc_final: 0.8787 (mtp85) REVERT: K 1092 ILE cc_start: 0.4144 (mm) cc_final: 0.3889 (mm) REVERT: K 1124 MET cc_start: 0.3445 (tpt) cc_final: 0.3216 (tpt) REVERT: K 1137 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.5310 (pmt170) REVERT: K 1234 ARG cc_start: 0.2631 (ptm160) cc_final: 0.2214 (tpt170) REVERT: K 1339 MET cc_start: -0.1974 (mmt) cc_final: -0.4051 (ttt) REVERT: K 1470 MET cc_start: 0.0719 (ppp) cc_final: 0.0189 (ppp) outliers start: 26 outliers final: 17 residues processed: 171 average time/residue: 0.3668 time to fit residues: 91.6588 Evaluate side-chains 169 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 1137 ARG 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 142 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17333 Z= 0.296 Angle : 0.538 7.109 24658 Z= 0.311 Chirality : 0.033 0.148 2747 Planarity : 0.003 0.032 2138 Dihedral : 28.541 174.233 4615 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 42.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.02 % Allowed : 20.07 % Favored : 76.91 % 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: 1.92 (0.24), residues: 1280 helix: 2.26 (0.19), residues: 776 sheet: -0.21 (0.67), residues: 70 loop : -0.27 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K1466 HIS 0.007 0.001 HIS F 75 PHE 0.015 0.001 PHE K1403 TYR 0.042 0.002 TYR B 88 ARG 0.002 0.000 ARG E 116 *********************** 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 180 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 73 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9373 (p) REVERT: C 64 GLU cc_start: 0.8791 (tt0) cc_final: 0.8495 (tm-30) REVERT: C 91 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 35 GLU cc_start: 0.7591 (pp20) cc_final: 0.7343 (pp20) REVERT: D 76 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8821 (mm-30) REVERT: D 92 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8751 (mtm-85) REVERT: E 122 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8734 (tptp) REVERT: F 88 TYR cc_start: 0.8865 (m-80) cc_final: 0.8635 (m-80) REVERT: G 56 GLU cc_start: 0.8707 (tt0) cc_final: 0.8200 (tm-30) REVERT: G 64 GLU cc_start: 0.8926 (tp30) cc_final: 0.8437 (tm-30) REVERT: H 34 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8456 (mtpt) REVERT: H 99 ARG cc_start: 0.9133 (mmm-85) cc_final: 0.8813 (mtp85) REVERT: K 1092 ILE cc_start: 0.4305 (mm) cc_final: 0.4077 (mm) REVERT: K 1137 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.4997 (pmt170) REVERT: K 1234 ARG cc_start: 0.2752 (ptm160) cc_final: 0.2335 (tpt170) REVERT: K 1339 MET cc_start: -0.1681 (mmt) cc_final: -0.3950 (ttt) REVERT: K 1470 MET cc_start: 0.1027 (ppp) cc_final: 0.0317 (ppp) outliers start: 34 outliers final: 25 residues processed: 171 average time/residue: 0.3593 time to fit residues: 91.0948 Evaluate side-chains 175 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1098 ASP Chi-restraints excluded: chain K residue 1137 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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** K1481 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17333 Z= 0.269 Angle : 0.517 8.419 24658 Z= 0.302 Chirality : 0.033 0.145 2747 Planarity : 0.003 0.032 2138 Dihedral : 28.533 172.158 4615 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 42.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.58 % Allowed : 20.43 % Favored : 77.00 % 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: 1.91 (0.24), residues: 1280 helix: 2.27 (0.19), residues: 777 sheet: -0.24 (0.67), residues: 70 loop : -0.31 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K1466 HIS 0.005 0.001 HIS F 75 PHE 0.018 0.001 PHE K1403 TYR 0.029 0.002 TYR B 88 ARG 0.002 0.000 ARG K1137 ********************** 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 fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8251 (mm-30) REVERT: B 73 THR cc_start: 0.9632 (OUTLIER) cc_final: 0.9350 (p) REVERT: C 64 GLU cc_start: 0.8802 (tt0) cc_final: 0.8513 (tm-30) REVERT: C 91 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8119 (tm-30) REVERT: D 35 GLU cc_start: 0.7562 (pp20) cc_final: 0.7319 (pp20) REVERT: D 92 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8755 (mtm-85) REVERT: E 122 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8789 (tptp) REVERT: F 88 TYR cc_start: 0.8924 (m-80) cc_final: 0.8713 (m-80) REVERT: G 56 GLU cc_start: 0.8694 (tt0) cc_final: 0.8180 (tm-30) REVERT: G 64 GLU cc_start: 0.8911 (tp30) cc_final: 0.8491 (tm-30) REVERT: H 34 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8462 (mtpt) REVERT: K 1092 ILE cc_start: 0.4394 (mm) cc_final: 0.4166 (mm) REVERT: K 1137 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.5034 (pmt170) REVERT: K 1234 ARG cc_start: 0.2749 (ptm160) cc_final: 0.2371 (tpt170) REVERT: K 1339 MET cc_start: -0.1675 (mmt) cc_final: -0.3925 (ttt) REVERT: K 1470 MET cc_start: 0.1071 (ppp) cc_final: 0.0369 (ppp) outliers start: 29 outliers final: 24 residues processed: 167 average time/residue: 0.3443 time to fit residues: 86.1849 Evaluate side-chains 174 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 1137 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057141 restraints weight = 86750.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058276 restraints weight = 48437.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058943 restraints weight = 35117.033| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17333 Z= 0.162 Angle : 0.457 5.911 24658 Z= 0.274 Chirality : 0.031 0.141 2747 Planarity : 0.003 0.031 2138 Dihedral : 28.393 172.672 4615 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 38.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.69 % Allowed : 21.31 % Favored : 77.00 % 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: 2.40 (0.24), residues: 1280 helix: 2.68 (0.19), residues: 777 sheet: -0.19 (0.67), residues: 70 loop : -0.12 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1466 HIS 0.005 0.001 HIS F 75 PHE 0.019 0.001 PHE K1403 TYR 0.024 0.001 TYR B 88 ARG 0.002 0.000 ARG E 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.82 seconds wall clock time: 72 minutes 54.08 seconds (4374.08 seconds total)