Starting phenix.real_space_refine on Tue Dec 31 19:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vaa_43087/12_2024/8vaa_43087_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vaa_43087/12_2024/8vaa_43087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vaa_43087/12_2024/8vaa_43087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vaa_43087/12_2024/8vaa_43087.map" model { file = "/net/cci-nas-00/data/ceres_data/8vaa_43087/12_2024/8vaa_43087_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vaa_43087/12_2024/8vaa_43087_trim.cif" } resolution = 3.58 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= 0.012 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: 7 Type Number sf(0) Gaussians P 20 5.49 5 Mg 10 5.21 5 S 210 5.16 5 C 21890 2.51 5 N 5900 2.21 5 O 6710 1.98 5 H 33030 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 67770 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "F" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "G" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "J" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5609 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "K" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "N" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "O" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "P" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Q" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "S" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "T" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.23, per 1000 atoms: 0.40 Number of scatterers: 67770 At special positions: 0 Unit cell: (135.779, 139.944, 340.697, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 210 16.00 P 20 15.00 Mg 10 11.99 O 6710 8.00 N 5900 7.00 C 21890 6.00 H 33030 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.15 Conformation dependent library (CDL) restraints added in 4.4 seconds 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8180 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 54 sheets defined 55.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.753A pdb=" N GLN A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.670A pdb=" N MET A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.153A pdb=" N ARG A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.717A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 204 through 218 Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.640A pdb=" N GLU A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.702A pdb=" N ILE A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.537A pdb=" N THR A 306 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.372A pdb=" N LYS A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.747A pdb=" N GLN B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.686A pdb=" N MET B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 4.143A pdb=" N ARG B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.717A pdb=" N SER B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 204 through 218 Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.665A pdb=" N GLU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.620A pdb=" N ILE B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.552A pdb=" N THR B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.361A pdb=" N LYS B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.865A pdb=" N GLN C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.617A pdb=" N MET C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 4.107A pdb=" N ARG C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 148 removed outlier: 3.739A pdb=" N SER C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 204 through 218 Processing helix chain 'C' and resid 224 through 235 removed outlier: 3.641A pdb=" N GLU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.559A pdb=" N ILE C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 287 through 290 removed outlier: 6.389A pdb=" N ASP C 290 " --> pdb=" O CYS C 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 287 through 290' Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 4.250A pdb=" N TYR C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.365A pdb=" N LYS C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.818A pdb=" N GLN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 removed outlier: 3.643A pdb=" N MET D 84 " --> pdb=" O ASN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 removed outlier: 4.166A pdb=" N ARG D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 removed outlier: 3.753A pdb=" N SER D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 224 through 235 removed outlier: 3.566A pdb=" N GLU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.560A pdb=" N ILE D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.618A pdb=" N THR D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR D 308 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 370 through 375 removed outlier: 4.370A pdb=" N LYS D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.749A pdb=" N GLN E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.777A pdb=" N MET E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 127 removed outlier: 4.117A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.728A pdb=" N SER E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 204 through 218 Processing helix chain 'E' and resid 224 through 235 removed outlier: 3.629A pdb=" N GLU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 259 through 264 Processing helix chain 'E' and resid 265 through 270 removed outlier: 3.607A pdb=" N ILE E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 303 through 308 removed outlier: 3.684A pdb=" N THR E 306 " --> pdb=" O GLY E 303 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR E 308 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 361 through 368 Processing helix chain 'E' and resid 369 through 376 removed outlier: 3.568A pdb=" N VAL E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 375 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.755A pdb=" N GLN F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 93 removed outlier: 3.512A pdb=" N LYS F 86 " --> pdb=" O ASP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 127 removed outlier: 4.118A pdb=" N ARG F 118 " --> pdb=" O PRO F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 148 removed outlier: 3.712A pdb=" N SER F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 204 through 218 Processing helix chain 'F' and resid 224 through 235 removed outlier: 3.625A pdb=" N GLU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.526A pdb=" N ARG F 258 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 254 through 259' Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 265 through 269 removed outlier: 3.581A pdb=" N ILE F 269 " --> pdb=" O PRO F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 303 through 308 removed outlier: 4.199A pdb=" N TYR F 308 " --> pdb=" O THR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 361 through 368 Processing helix chain 'F' and resid 370 through 375 removed outlier: 4.341A pdb=" N LYS F 375 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.712A pdb=" N GLN G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.664A pdb=" N MET G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 127 removed outlier: 4.093A pdb=" N ARG G 118 " --> pdb=" O PRO G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 148 removed outlier: 3.686A pdb=" N SER G 143 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 196 Processing helix chain 'G' and resid 204 through 218 Processing helix chain 'G' and resid 224 through 235 removed outlier: 3.615A pdb=" N GLU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 257 Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 275 through 286 Processing helix chain 'G' and resid 291 through 298 Processing helix chain 'G' and resid 303 through 308 removed outlier: 3.595A pdb=" N THR G 306 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR G 308 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 323 Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 339 through 351 Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 361 through 368 Processing helix chain 'G' and resid 370 through 375 removed outlier: 4.337A pdb=" N LYS G 375 " --> pdb=" O ILE G 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 63 removed outlier: 3.724A pdb=" N GLN H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 93 removed outlier: 3.647A pdb=" N MET H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 127 removed outlier: 4.159A pdb=" N ARG H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.770A pdb=" N SER H 143 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 196 Processing helix chain 'H' and resid 204 through 218 Processing helix chain 'H' and resid 224 through 235 removed outlier: 3.637A pdb=" N GLU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 257 Processing helix chain 'H' and resid 259 through 264 Processing helix chain 'H' and resid 265 through 270 removed outlier: 3.627A pdb=" N ILE H 269 " --> pdb=" O PRO H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 286 Processing helix chain 'H' and resid 291 through 298 Processing helix chain 'H' and resid 303 through 308 removed outlier: 3.602A pdb=" N THR H 306 " --> pdb=" O GLY H 303 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR H 308 " --> pdb=" O THR H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 323 Processing helix chain 'H' and resid 336 through 338 No H-bonds generated for 'chain 'H' and resid 336 through 338' Processing helix chain 'H' and resid 339 through 351 Processing helix chain 'H' and resid 352 through 357 Processing helix chain 'H' and resid 361 through 368 Processing helix chain 'H' and resid 370 through 375 removed outlier: 4.361A pdb=" N LYS H 375 " --> pdb=" O ILE H 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 removed outlier: 3.782A pdb=" N GLN I 61 " --> pdb=" O GLY I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.661A pdb=" N MET I 84 " --> pdb=" O ASN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 127 removed outlier: 4.159A pdb=" N ARG I 118 " --> pdb=" O PRO I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 148 removed outlier: 3.771A pdb=" N SER I 143 " --> pdb=" O GLN I 139 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU I 144 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR I 145 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 196 Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 224 through 235 removed outlier: 3.669A pdb=" N GLU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 257 Processing helix chain 'I' and resid 259 through 264 Processing helix chain 'I' and resid 265 through 269 removed outlier: 3.613A pdb=" N ILE I 269 " --> pdb=" O PRO I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 286 Processing helix chain 'I' and resid 291 through 298 Processing helix chain 'I' and resid 303 through 308 removed outlier: 3.622A pdb=" N THR I 306 " --> pdb=" O GLY I 303 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR I 308 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 323 Processing helix chain 'I' and resid 336 through 338 No H-bonds generated for 'chain 'I' and resid 336 through 338' Processing helix chain 'I' and resid 339 through 351 Processing helix chain 'I' and resid 352 through 357 Processing helix chain 'I' and resid 361 through 368 Processing helix chain 'I' and resid 370 through 375 removed outlier: 4.345A pdb=" N LYS I 375 " --> pdb=" O ILE I 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 63 removed outlier: 3.752A pdb=" N GLN J 61 " --> pdb=" O GLY J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 93 removed outlier: 3.665A pdb=" N MET J 84 " --> pdb=" O ASN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 127 removed outlier: 4.188A pdb=" N ARG J 118 " --> pdb=" O PRO J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 148 removed outlier: 3.766A pdb=" N SER J 143 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 196 Processing helix chain 'J' and resid 197 through 199 No H-bonds generated for 'chain 'J' and resid 197 through 199' Processing helix chain 'J' and resid 204 through 218 Processing helix chain 'J' and resid 224 through 235 removed outlier: 3.603A pdb=" N GLU J 228 " --> pdb=" O ASP J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 Processing helix chain 'J' and resid 259 through 264 Processing helix chain 'J' and resid 265 through 270 removed outlier: 3.604A pdb=" N ILE J 269 " --> pdb=" O PRO J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 286 Processing helix chain 'J' and resid 291 through 298 Processing helix chain 'J' and resid 303 through 308 removed outlier: 3.530A pdb=" N THR J 306 " --> pdb=" O GLY J 303 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR J 308 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 339 through 351 Processing helix chain 'J' and resid 352 through 357 Processing helix chain 'J' and resid 361 through 368 Processing helix chain 'J' and resid 370 through 375 removed outlier: 4.346A pdb=" N LYS J 375 " --> pdb=" O ILE J 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 244 removed outlier: 3.534A pdb=" N ALA K 233 " --> pdb=" O GLY K 229 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS K 243 " --> pdb=" O ASN K 239 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU K 244 " --> pdb=" O TYR K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 280 removed outlier: 3.603A pdb=" N THR K 253 " --> pdb=" O PRO K 249 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 256 " --> pdb=" O LYS K 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 244 removed outlier: 3.529A pdb=" N ALA L 233 " --> pdb=" O GLY L 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS L 243 " --> pdb=" O ASN L 239 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU L 244 " --> pdb=" O TYR L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 280 removed outlier: 3.607A pdb=" N THR L 253 " --> pdb=" O PRO L 249 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE L 256 " --> pdb=" O LYS L 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 244 removed outlier: 3.523A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS M 243 " --> pdb=" O ASN M 239 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU M 244 " --> pdb=" O TYR M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 280 removed outlier: 3.584A pdb=" N THR M 253 " --> pdb=" O PRO M 249 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE M 256 " --> pdb=" O LYS M 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 244 removed outlier: 3.547A pdb=" N ALA N 233 " --> pdb=" O GLY N 229 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS N 243 " --> pdb=" O ASN N 239 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU N 244 " --> pdb=" O TYR N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 280 removed outlier: 3.607A pdb=" N THR N 253 " --> pdb=" O PRO N 249 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE N 256 " --> pdb=" O LYS N 252 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 244 removed outlier: 3.552A pdb=" N ALA O 233 " --> pdb=" O GLY O 229 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS O 243 " --> pdb=" O ASN O 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU O 244 " --> pdb=" O TYR O 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 280 removed outlier: 3.602A pdb=" N THR O 253 " --> pdb=" O PRO O 249 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE O 256 " --> pdb=" O LYS O 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 244 removed outlier: 3.568A pdb=" N ALA P 233 " --> pdb=" O GLY P 229 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS P 243 " --> pdb=" O ASN P 239 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 280 removed outlier: 3.605A pdb=" N THR P 253 " --> pdb=" O PRO P 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE P 256 " --> pdb=" O LYS P 252 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 244 removed outlier: 3.539A pdb=" N ALA Q 233 " --> pdb=" O GLY Q 229 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS Q 243 " --> pdb=" O ASN Q 239 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU Q 244 " --> pdb=" O TYR Q 240 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 280 removed outlier: 3.603A pdb=" N THR Q 253 " --> pdb=" O PRO Q 249 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE Q 256 " --> pdb=" O LYS Q 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 244 removed outlier: 3.543A pdb=" N ALA R 233 " --> pdb=" O GLY R 229 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS R 243 " --> pdb=" O ASN R 239 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU R 244 " --> pdb=" O TYR R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 280 removed outlier: 3.601A pdb=" N THR R 253 " --> pdb=" O PRO R 249 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 256 " --> pdb=" O LYS R 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 244 removed outlier: 3.529A pdb=" N ALA S 233 " --> pdb=" O GLY S 229 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS S 243 " --> pdb=" O ASN S 239 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU S 244 " --> pdb=" O TYR S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 280 removed outlier: 3.615A pdb=" N THR S 253 " --> pdb=" O PRO S 249 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE S 256 " --> pdb=" O LYS S 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 244 removed outlier: 3.582A pdb=" N ALA T 233 " --> pdb=" O GLY T 229 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS T 243 " --> pdb=" O ASN T 239 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU T 244 " --> pdb=" O TYR T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 248 through 280 removed outlier: 3.603A pdb=" N THR T 253 " --> pdb=" O PRO T 249 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE T 256 " --> pdb=" O LYS T 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.690A pdb=" N LYS A 20 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 22 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 108 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASN A 14 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 134 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 3.623A pdb=" N ARG A 39 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.750A pdb=" N TYR A 168 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.750A pdb=" N TYR A 168 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 153 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.664A pdb=" N LYS B 20 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 22 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 108 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN B 14 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 134 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 359 " --> pdb=" O MET B 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.676A pdb=" N ARG B 39 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 180 removed outlier: 6.490A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB3, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.649A pdb=" N LYS C 20 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 134 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.687A pdb=" N ARG C 39 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB6, first strand: chain 'C' and resid 178 through 180 removed outlier: 6.393A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AB8, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.707A pdb=" N LYS D 20 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 22 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR D 108 " --> pdb=" O CYS D 12 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASN D 14 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET D 134 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.629A pdb=" N ARG D 39 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 73 through 74 Processing sheet with id=AC2, first strand: chain 'D' and resid 178 through 180 removed outlier: 3.515A pdb=" N VAL D 154 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN D 299 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AC4, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.740A pdb=" N LYS E 20 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 22 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR E 108 " --> pdb=" O CYS E 12 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN E 14 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET E 134 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 55 through 56 removed outlier: 3.636A pdb=" N ARG E 39 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 73 through 74 Processing sheet with id=AC7, first strand: chain 'E' and resid 178 through 180 removed outlier: 3.534A pdb=" N VAL E 165 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 154 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE E 153 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN E 299 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 33 removed outlier: 3.697A pdb=" N LYS F 20 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY F 22 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR F 108 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASN F 14 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET F 134 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 359 " --> pdb=" O MET F 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 55 through 56 removed outlier: 3.588A pdb=" N ARG F 39 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 73 through 74 Processing sheet with id=AD3, first strand: chain 'F' and resid 152 through 154 removed outlier: 3.531A pdb=" N VAL F 165 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 240 through 243 Processing sheet with id=AD5, first strand: chain 'F' and resid 299 through 300 removed outlier: 6.210A pdb=" N ASN F 299 " --> pdb=" O ILE F 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 removed outlier: 3.713A pdb=" N LYS G 20 " --> pdb=" O ASP G 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY G 22 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR G 108 " --> pdb=" O CYS G 12 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN G 14 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET G 134 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 359 " --> pdb=" O MET G 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 55 through 56 removed outlier: 3.643A pdb=" N ARG G 39 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 73 through 74 Processing sheet with id=AD9, first strand: chain 'G' and resid 171 through 172 removed outlier: 3.795A pdb=" N TYR G 168 " --> pdb=" O TYR G 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 171 through 172 removed outlier: 3.795A pdb=" N TYR G 168 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 165 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 154 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE G 153 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN G 299 " --> pdb=" O ILE G 332 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 240 through 243 Processing sheet with id=AE3, first strand: chain 'H' and resid 31 through 33 removed outlier: 4.013A pdb=" N LYS H 20 " --> pdb=" O ASP H 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 22 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR H 108 " --> pdb=" O CYS H 12 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN H 14 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET H 134 " --> pdb=" O ILE H 359 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 55 through 56 removed outlier: 3.644A pdb=" N ARG H 39 " --> pdb=" O THR H 68 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 73 through 74 Processing sheet with id=AE6, first strand: chain 'H' and resid 171 through 172 removed outlier: 3.804A pdb=" N TYR H 168 " --> pdb=" O TYR H 171 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 171 through 172 removed outlier: 3.804A pdb=" N TYR H 168 " --> pdb=" O TYR H 171 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE H 153 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER H 302 " --> pdb=" O ILE H 153 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU H 155 " --> pdb=" O SER H 302 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASN H 299 " --> pdb=" O ILE H 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 240 through 243 Processing sheet with id=AE9, first strand: chain 'I' and resid 31 through 33 removed outlier: 3.523A pdb=" N GLY I 22 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR I 108 " --> pdb=" O CYS I 12 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET I 134 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE I 359 " --> pdb=" O MET I 134 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 55 through 56 removed outlier: 3.634A pdb=" N ARG I 39 " --> pdb=" O THR I 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 73 through 74 Processing sheet with id=AF3, first strand: chain 'I' and resid 178 through 180 removed outlier: 3.631A pdb=" N ASP I 156 " --> pdb=" O HIS I 163 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL I 165 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE I 153 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N SER I 302 " --> pdb=" O ILE I 153 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU I 155 " --> pdb=" O SER I 302 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN I 299 " --> pdb=" O ILE I 332 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 240 through 243 Processing sheet with id=AF5, first strand: chain 'J' and resid 31 through 33 removed outlier: 3.692A pdb=" N LYS J 20 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR J 108 " --> pdb=" O CYS J 12 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN J 14 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET J 134 " --> pdb=" O ILE J 359 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 55 through 56 removed outlier: 3.641A pdb=" N ARG J 39 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 73 through 74 Processing sheet with id=AF8, first strand: chain 'J' and resid 178 through 180 removed outlier: 3.647A pdb=" N ASP J 156 " --> pdb=" O HIS J 163 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL J 165 " --> pdb=" O VAL J 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL J 154 " --> pdb=" O VAL J 165 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE J 153 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER J 302 " --> pdb=" O ILE J 153 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU J 155 " --> pdb=" O SER J 302 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN J 299 " --> pdb=" O ILE J 332 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 240 through 243 1809 hydrogen bonds defined for protein. 4770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.92 Time building geometry restraints manager: 17.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32990 1.03 - 1.23: 89 1.23 - 1.42: 14223 1.42 - 1.62: 20778 1.62 - 1.81: 370 Bond restraints: 68450 Sorted by residual: bond pdb=" N CYS I 12 " pdb=" CA CYS I 12 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.23e-02 6.61e+03 7.64e+00 bond pdb=" N GLN B 51 " pdb=" CA GLN B 51 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" N CYS I 12 " pdb=" H CYS I 12 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" N CYS H 12 " pdb=" H CYS H 12 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" N THR H 108 " pdb=" H THR H 108 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 68445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 119203 1.38 - 2.76: 3751 2.76 - 4.14: 453 4.14 - 5.52: 89 5.52 - 6.90: 14 Bond angle restraints: 123510 Sorted by residual: angle pdb=" N MET F 84 " pdb=" CA MET F 84 " pdb=" C MET F 84 " ideal model delta sigma weight residual 111.82 107.19 4.63 1.16e+00 7.43e-01 1.59e+01 angle pdb=" CA MET H 49 " pdb=" C MET H 49 " pdb=" O MET H 49 " ideal model delta sigma weight residual 120.82 116.74 4.08 1.05e+00 9.07e-01 1.51e+01 angle pdb=" CA ASP C 53 " pdb=" C ASP C 53 " pdb=" O ASP C 53 " ideal model delta sigma weight residual 120.42 116.38 4.04 1.06e+00 8.90e-01 1.45e+01 angle pdb=" N LYS A 52 " pdb=" CA LYS A 52 " pdb=" C LYS A 52 " ideal model delta sigma weight residual 110.32 104.35 5.97 1.59e+00 3.96e-01 1.41e+01 angle pdb=" CA GLN H 51 " pdb=" C GLN H 51 " pdb=" O GLN H 51 " ideal model delta sigma weight residual 120.60 116.37 4.23 1.13e+00 7.83e-01 1.40e+01 ... (remaining 123505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 28367 17.98 - 35.96: 2965 35.96 - 53.94: 810 53.94 - 71.92: 214 71.92 - 89.90: 34 Dihedral angle restraints: 32390 sinusoidal: 17860 harmonic: 14530 Sorted by residual: dihedral pdb=" CA ASP E 224 " pdb=" C ASP E 224 " pdb=" N PHE E 225 " pdb=" CA PHE E 225 " ideal model delta harmonic sigma weight residual 180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASN C 14 " pdb=" CB ASN C 14 " pdb=" CG ASN C 14 " pdb=" OD1 ASN C 14 " ideal model delta sinusoidal sigma weight residual -90.00 -157.42 67.42 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CB GLU K 268 " pdb=" CG GLU K 268 " pdb=" CD GLU K 268 " pdb=" OE1 GLU K 268 " ideal model delta sinusoidal sigma weight residual 0.00 -86.49 86.49 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 32387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3797 0.035 - 0.070: 1114 0.070 - 0.105: 356 0.105 - 0.139: 160 0.139 - 0.174: 3 Chirality restraints: 5430 Sorted by residual: chirality pdb=" CA LEU H 107 " pdb=" N LEU H 107 " pdb=" C LEU H 107 " pdb=" CB LEU H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA GLN M 267 " pdb=" N GLN M 267 " pdb=" C GLN M 267 " pdb=" CB GLN M 267 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA GLN L 267 " pdb=" N GLN L 267 " pdb=" C GLN L 267 " pdb=" CB GLN L 267 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 5427 not shown) Planarity restraints: 10250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 51 " 0.026 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN A 51 " -0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN A 51 " -0.025 2.00e-02 2.50e+03 pdb=" NE2 GLN A 51 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 51 " 0.766 2.00e-02 2.50e+03 pdb="HE22 GLN A 51 " -0.764 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 51 " 0.159 2.00e-02 2.50e+03 4.26e-01 2.72e+03 pdb=" CD GLN C 51 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C 51 " -0.152 2.00e-02 2.50e+03 pdb=" NE2 GLN C 51 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 51 " 0.726 2.00e-02 2.50e+03 pdb="HE22 GLN C 51 " -0.717 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 51 " 0.204 2.00e-02 2.50e+03 4.11e-01 2.53e+03 pdb=" CD GLN B 51 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN B 51 " -0.196 2.00e-02 2.50e+03 pdb=" NE2 GLN B 51 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN B 51 " 0.688 2.00e-02 2.50e+03 pdb="HE22 GLN B 51 " -0.678 2.00e-02 2.50e+03 ... (remaining 10247 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 314 2.01 - 2.65: 89994 2.65 - 3.30: 189238 3.30 - 3.95: 231709 3.95 - 4.60: 372474 Nonbonded interactions: 883729 Sorted by model distance: nonbonded pdb=" O ASN C 14 " pdb="HD21 ASN C 14 " model vdw 1.357 2.450 nonbonded pdb=" OE2 GLU F 261 " pdb="HH22 ARG F 314 " model vdw 1.616 2.450 nonbonded pdb=" OD1 ASP J 13 " pdb=" HG1 THR J 108 " model vdw 1.626 2.450 nonbonded pdb=" H VAL D 203 " pdb=" OE1 GLU D 207 " model vdw 1.636 2.450 nonbonded pdb="HH11 ARG D 292 " pdb=" OD2 ASP F 246 " model vdw 1.638 2.450 ... (remaining 883724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 9.180 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: 0.990 Extract box with map and model: 2.330 Check model and map are aligned: 0.410 Set scattering table: 0.510 Process input model: 117.600 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.003 0.034 35420 Z= 0.209 Angle : 0.639 6.899 47990 Z= 0.343 Chirality : 0.040 0.174 5430 Planarity : 0.005 0.069 6110 Dihedral : 16.298 89.896 13350 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.26 % Allowed : 0.37 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.13), residues: 4350 helix: 1.72 (0.11), residues: 2100 sheet: -1.41 (0.20), residues: 650 loop : -1.64 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 342 HIS 0.006 0.001 HIS H 277 PHE 0.014 0.001 PHE C 354 TYR 0.021 0.001 TYR H 281 ARG 0.010 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 401 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: N 274 ASN cc_start: 0.7989 (m-40) cc_final: 0.7430 (m-40) outliers start: 10 outliers final: 0 residues processed: 406 average time/residue: 1.0362 time to fit residues: 632.2126 Evaluate side-chains 321 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 337 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 390 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 265 GLN E 51 GLN E 265 GLN F 265 GLN J 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35420 Z= 0.261 Angle : 0.589 6.302 47990 Z= 0.297 Chirality : 0.040 0.134 5430 Planarity : 0.004 0.043 6110 Dihedral : 4.795 36.757 4840 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.37 % Allowed : 5.90 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.13), residues: 4350 helix: 2.72 (0.11), residues: 2030 sheet: -1.24 (0.20), residues: 650 loop : -1.26 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 342 HIS 0.004 0.001 HIS D 277 PHE 0.008 0.001 PHE J 354 TYR 0.010 0.001 TYR P 240 ARG 0.004 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 349 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 335 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 119 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: N 221 GLU cc_start: 0.8065 (tp30) cc_final: 0.7818 (tp30) outliers start: 14 outliers final: 4 residues processed: 347 average time/residue: 1.0169 time to fit residues: 536.9846 Evaluate side-chains 319 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 314 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 277 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 217 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 391 optimal weight: 0.8980 chunk 422 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 313 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 14 ASN C 265 GLN H 265 GLN I 265 GLN Q 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35420 Z= 0.156 Angle : 0.540 6.483 47990 Z= 0.264 Chirality : 0.039 0.129 5430 Planarity : 0.004 0.040 6110 Dihedral : 4.568 30.903 4840 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.29 % Allowed : 6.56 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.13), residues: 4350 helix: 2.99 (0.11), residues: 2050 sheet: -1.07 (0.20), residues: 650 loop : -0.93 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 81 HIS 0.004 0.001 HIS F 277 PHE 0.006 0.001 PHE C 354 TYR 0.009 0.001 TYR P 240 ARG 0.004 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 322 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 MET cc_start: 0.7701 (tpt) cc_final: 0.7479 (tpt) REVERT: J 119 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: N 221 GLU cc_start: 0.8021 (tp30) cc_final: 0.7763 (tp30) outliers start: 11 outliers final: 8 residues processed: 328 average time/residue: 1.0559 time to fit residues: 528.7717 Evaluate side-chains 321 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 312 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain P residue 267 GLN Chi-restraints excluded: chain S residue 278 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 386 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 392 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 HIS C 163 HIS D 163 HIS ** M 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 274 ASN R 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35420 Z= 0.319 Angle : 0.580 6.286 47990 Z= 0.292 Chirality : 0.040 0.132 5430 Planarity : 0.004 0.043 6110 Dihedral : 4.659 39.862 4840 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.58 % Allowed : 7.35 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.13), residues: 4350 helix: 2.95 (0.11), residues: 2050 sheet: -0.96 (0.20), residues: 650 loop : -0.82 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 81 HIS 0.004 0.001 HIS F 373 PHE 0.007 0.001 PHE H 129 TYR 0.012 0.001 TYR I 281 ARG 0.003 0.001 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 316 time to evaluate : 4.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7835 (tpt) cc_final: 0.7577 (tpt) REVERT: G 301 MET cc_start: 0.7806 (mmm) cc_final: 0.7384 (mtt) REVERT: J 119 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: N 221 GLU cc_start: 0.8100 (tp30) cc_final: 0.7833 (tp30) outliers start: 22 outliers final: 16 residues processed: 328 average time/residue: 1.0452 time to fit residues: 523.1700 Evaluate side-chains 329 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 312 time to evaluate : 4.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 267 GLN Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 278 GLU Chi-restraints excluded: chain T residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 346 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 0.1980 chunk 354 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS E 163 HIS ** M 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35420 Z= 0.213 Angle : 0.544 5.940 47990 Z= 0.267 Chirality : 0.039 0.129 5430 Planarity : 0.003 0.049 6110 Dihedral : 4.554 32.203 4840 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.53 % Allowed : 7.72 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.13), residues: 4350 helix: 2.84 (0.11), residues: 2120 sheet: -0.85 (0.21), residues: 650 loop : -0.61 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 81 HIS 0.003 0.001 HIS F 373 PHE 0.008 0.001 PHE H 129 TYR 0.016 0.001 TYR I 281 ARG 0.003 0.000 ARG I 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 4.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 301 MET cc_start: 0.7788 (mmm) cc_final: 0.7423 (mtt) REVERT: J 119 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: N 212 ASP cc_start: 0.5202 (p0) cc_final: 0.4920 (p0) REVERT: N 221 GLU cc_start: 0.8057 (tp30) cc_final: 0.7823 (tp30) outliers start: 20 outliers final: 12 residues processed: 329 average time/residue: 1.0697 time to fit residues: 540.6713 Evaluate side-chains 322 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 309 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 267 GLN Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain T residue 238 ILE Chi-restraints excluded: chain T residue 278 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 139 optimal weight: 3.9990 chunk 374 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 416 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35420 Z= 0.226 Angle : 0.545 5.667 47990 Z= 0.268 Chirality : 0.039 0.129 5430 Planarity : 0.003 0.043 6110 Dihedral : 4.495 36.028 4840 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.56 % Allowed : 7.88 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.14), residues: 4350 helix: 2.84 (0.11), residues: 2120 sheet: -0.71 (0.21), residues: 650 loop : -0.50 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 81 HIS 0.003 0.001 HIS F 373 PHE 0.008 0.001 PHE H 129 TYR 0.013 0.001 TYR I 281 ARG 0.003 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 4.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8637 (mmm) cc_final: 0.8269 (mmt) REVERT: G 301 MET cc_start: 0.7818 (mmm) cc_final: 0.7458 (mtt) REVERT: J 119 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: N 212 ASP cc_start: 0.5279 (p0) cc_final: 0.4944 (p0) REVERT: N 221 GLU cc_start: 0.8017 (tp30) cc_final: 0.7796 (tp30) outliers start: 21 outliers final: 15 residues processed: 327 average time/residue: 1.0251 time to fit residues: 510.8171 Evaluate side-chains 327 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 267 GLN Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 278 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 401 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 350 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 252 optimal weight: 0.0050 chunk 191 optimal weight: 3.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 HIS Q 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35420 Z= 0.225 Angle : 0.543 5.680 47990 Z= 0.267 Chirality : 0.039 0.126 5430 Planarity : 0.003 0.037 6110 Dihedral : 4.480 34.905 4840 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.53 % Allowed : 8.28 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.14), residues: 4350 helix: 2.87 (0.12), residues: 2120 sheet: -0.63 (0.21), residues: 650 loop : -0.42 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 81 HIS 0.003 0.001 HIS G 373 PHE 0.008 0.001 PHE F 129 TYR 0.013 0.001 TYR E 281 ARG 0.003 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8639 (mmm) cc_final: 0.8275 (mmt) REVERT: G 301 MET cc_start: 0.7816 (mmm) cc_final: 0.7465 (mtt) REVERT: J 119 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: N 212 ASP cc_start: 0.5258 (p0) cc_final: 0.4905 (p0) REVERT: N 221 GLU cc_start: 0.7993 (tp30) cc_final: 0.7785 (tp30) outliers start: 20 outliers final: 16 residues processed: 327 average time/residue: 0.9966 time to fit residues: 498.0491 Evaluate side-chains 326 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 309 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 267 GLN Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 257 GLU Chi-restraints excluded: chain S residue 278 GLU Chi-restraints excluded: chain T residue 238 ILE Chi-restraints excluded: chain T residue 278 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 256 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35420 Z= 0.272 Angle : 0.562 6.954 47990 Z= 0.278 Chirality : 0.039 0.148 5430 Planarity : 0.003 0.036 6110 Dihedral : 4.526 38.631 4840 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.50 % Allowed : 8.68 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.14), residues: 4350 helix: 2.85 (0.11), residues: 2110 sheet: -0.63 (0.21), residues: 650 loop : -0.44 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 81 HIS 0.003 0.001 HIS J 277 PHE 0.009 0.001 PHE H 129 TYR 0.015 0.001 TYR E 281 ARG 0.003 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 311 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8683 (mmm) cc_final: 0.8316 (mmt) REVERT: G 301 MET cc_start: 0.7836 (mmm) cc_final: 0.7495 (mtt) REVERT: J 119 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: N 212 ASP cc_start: 0.5323 (p0) cc_final: 0.4982 (p0) outliers start: 19 outliers final: 17 residues processed: 320 average time/residue: 1.0185 time to fit residues: 495.3899 Evaluate side-chains 321 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 257 GLU Chi-restraints excluded: chain S residue 278 GLU Chi-restraints excluded: chain T residue 238 ILE Chi-restraints excluded: chain T residue 278 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 377 optimal weight: 8.9990 chunk 397 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 386 optimal weight: 0.0980 chunk 396 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35420 Z= 0.214 Angle : 0.548 6.457 47990 Z= 0.269 Chirality : 0.039 0.157 5430 Planarity : 0.003 0.034 6110 Dihedral : 4.492 36.673 4840 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.50 % Allowed : 8.70 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.80 (0.14), residues: 4350 helix: 2.85 (0.12), residues: 2120 sheet: -0.60 (0.21), residues: 650 loop : -0.33 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 81 HIS 0.003 0.001 HIS H 373 PHE 0.008 0.001 PHE H 129 TYR 0.014 0.001 TYR E 281 ARG 0.002 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 326 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 307 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 229 MET cc_start: 0.8668 (mmm) cc_final: 0.8303 (mmt) REVERT: G 301 MET cc_start: 0.7829 (mmm) cc_final: 0.7472 (mtt) REVERT: J 119 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: N 212 ASP cc_start: 0.5295 (p0) cc_final: 0.4960 (p0) outliers start: 19 outliers final: 18 residues processed: 317 average time/residue: 1.0063 time to fit residues: 488.2488 Evaluate side-chains 320 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain H residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 257 GLU Chi-restraints excluded: chain S residue 278 GLU Chi-restraints excluded: chain T residue 238 ILE Chi-restraints excluded: chain T residue 278 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 384 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 428 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35420 Z= 0.247 Angle : 0.560 6.478 47990 Z= 0.276 Chirality : 0.039 0.142 5430 Planarity : 0.003 0.034 6110 Dihedral : 4.502 39.304 4840 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.50 % Allowed : 8.94 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.14), residues: 4350 helix: 2.81 (0.12), residues: 2120 sheet: -0.62 (0.21), residues: 650 loop : -0.31 (0.17), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 81 HIS 0.003 0.001 HIS F 277 PHE 0.009 0.001 PHE H 129 TYR 0.013 0.001 TYR E 281 ARG 0.003 0.000 ARG E 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue MET 178 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ILE 269 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue ALA 349 is missing expected H atoms. Skipping. Residue THR 360 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8691 (mmm) cc_final: 0.8329 (mmt) REVERT: G 301 MET cc_start: 0.7826 (mmm) cc_final: 0.7465 (mtt) REVERT: J 119 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: N 212 ASP cc_start: 0.5266 (p0) cc_final: 0.4938 (p0) outliers start: 19 outliers final: 17 residues processed: 313 average time/residue: 1.0098 time to fit residues: 484.3177 Evaluate side-chains 318 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 300 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain H residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 277 HIS Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 257 GLU Chi-restraints excluded: chain S residue 278 GLU Chi-restraints excluded: chain T residue 238 ILE Chi-restraints excluded: chain T residue 278 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 209 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 363 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 341 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 350 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.028228 restraints weight = 701974.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.029349 restraints weight = 252794.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.030076 restraints weight = 140040.202| |-----------------------------------------------------------------------------| r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35420 Z= 0.228 Angle : 0.552 6.439 47990 Z= 0.272 Chirality : 0.039 0.148 5430 Planarity : 0.003 0.032 6110 Dihedral : 4.490 38.617 4840 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.53 % Allowed : 8.89 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.80 (0.14), residues: 4350 helix: 2.84 (0.12), residues: 2120 sheet: -0.70 (0.20), residues: 730 loop : -0.19 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 81 HIS 0.003 0.001 HIS H 373 PHE 0.008 0.001 PHE G 129 TYR 0.012 0.001 TYR E 281 ARG 0.002 0.000 ARG E 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11367.74 seconds wall clock time: 197 minutes 48.39 seconds (11868.39 seconds total)