Starting phenix.real_space_refine on Sat Feb 17 06:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghv_40052/02_2024/8ghv_40052_neut_trim_updated.pdb" } resolution = 2.8 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= 0.004 sd= 1.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1971 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 5308 2.51 5 N 1383 2.21 5 O 1492 1.98 5 H 7637 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "S GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3144 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 4847 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 698 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 3889 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 131 Chain: "S" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3269 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.44, per 1000 atoms: 0.47 Number of scatterers: 15874 At special positions: 0 Unit cell: (92.8789, 123.555, 132.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 1492 8.00 N 1383 7.00 C 5308 6.00 H 7637 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 32.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.477A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.738A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.671A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.883A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 140 removed outlier: 3.978A pdb=" N LEU D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 153 through 178 Processing helix chain 'D' and resid 186 through 219 removed outlier: 3.767A pdb=" N ILE D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 230 through 253 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 275 through 305 removed outlier: 3.887A pdb=" N SER D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 356 removed outlier: 4.113A pdb=" N LEU D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 373 through 399 removed outlier: 3.746A pdb=" N MET D 384 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 388 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Proline residue: D 394 - end of helix removed outlier: 3.869A pdb=" N ALA D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 411 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.738A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.012A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.083A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.863A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.122A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.863A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.710A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.590A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.520A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'S' and resid 214 through 218 removed outlier: 3.647A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1071 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: 5.48 Time building geometry restraints manager: 12.60 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: 7608 1.03 - 1.23: 136 1.23 - 1.43: 3448 1.43 - 1.62: 4778 1.62 - 1.82: 77 Bond restraints: 16047 Sorted by residual: bond pdb=" N VAL D 392 " pdb=" CA VAL D 392 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" C LEU B 79 " pdb=" O LEU B 79 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.14e-02 7.69e+03 1.45e+01 bond pdb=" N ILE D 395 " pdb=" CA ILE D 395 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.08e-02 8.57e+03 1.42e+01 bond pdb=" N VAL D 110 " pdb=" H VAL D 110 " ideal model delta sigma weight residual 0.860 0.931 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N TRP B 332 " pdb=" CA TRP B 332 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.32e-02 5.74e+03 9.39e+00 ... (remaining 16042 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.33: 91 104.33 - 111.79: 17696 111.79 - 119.25: 3959 119.25 - 126.71: 6919 126.71 - 134.18: 119 Bond angle restraints: 28784 Sorted by residual: angle pdb=" C12 ZI5 D 501 " pdb=" C10 ZI5 D 501 " pdb=" C9 ZI5 D 501 " ideal model delta sigma weight residual 85.91 123.03 -37.12 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C1 ZI5 D 501 " pdb=" C2 ZI5 D 501 " pdb=" C4 ZI5 D 501 " ideal model delta sigma weight residual 152.66 124.12 28.54 3.00e+00 1.11e-01 9.05e+01 angle pdb=" C13 ZI5 D 501 " pdb=" C11 ZI5 D 501 " pdb=" C8 ZI5 D 501 " ideal model delta sigma weight residual 152.65 124.53 28.12 3.00e+00 1.11e-01 8.79e+01 angle pdb=" C11 ZI5 D 501 " pdb=" C8 ZI5 D 501 " pdb=" C7 ZI5 D 501 " ideal model delta sigma weight residual 112.27 124.49 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C3 ZI5 D 501 " pdb=" C5 ZI5 D 501 " pdb=" C7 ZI5 D 501 " ideal model delta sigma weight residual 112.83 124.89 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 28779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 7369 26.04 - 52.07: 289 52.07 - 78.11: 37 78.11 - 104.14: 4 104.14 - 130.18: 1 Dihedral angle restraints: 7700 sinusoidal: 3831 harmonic: 3869 Sorted by residual: dihedral pdb=" C2 ZI5 D 501 " pdb=" C4 ZI5 D 501 " pdb=" C6 ZI5 D 501 " pdb=" C9 ZI5 D 501 " ideal model delta sinusoidal sigma weight residual 273.52 143.34 130.18 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CB CYS D 257 " pdb=" SG CYS D 257 " pdb=" SG CYS D 264 " pdb=" CB CYS D 264 " ideal model delta sinusoidal sigma weight residual -86.00 -120.33 34.33 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" SG CYS D 257 " pdb=" CB CYS D 264 " pdb=" SG CYS D 264 " pdb=" CA CYS D 264 " ideal model delta sinusoidal sigma weight residual -73.00 -13.90 -59.10 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 7697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 947 0.039 - 0.078: 254 0.078 - 0.117: 95 0.117 - 0.156: 57 0.156 - 0.195: 10 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CA ILE D 396 " pdb=" N ILE D 396 " pdb=" C ILE D 396 " pdb=" CB ILE D 396 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA ILE D 375 " pdb=" N ILE D 375 " pdb=" C ILE D 375 " pdb=" CB ILE D 375 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1360 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 176 " 0.218 2.00e-02 2.50e+03 2.53e-01 9.63e+02 pdb=" CD GLN B 176 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 176 " -0.211 2.00e-02 2.50e+03 pdb=" NE2 GLN B 176 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 176 " 0.387 2.00e-02 2.50e+03 pdb="HE22 GLN B 176 " -0.378 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 304 " -0.550 9.50e-02 1.11e+02 2.36e-01 5.29e+02 pdb=" NE ARG B 304 " -0.154 2.00e-02 2.50e+03 pdb=" CZ ARG B 304 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 304 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 304 " 0.029 2.00e-02 2.50e+03 pdb="HH11 ARG B 304 " 0.306 2.00e-02 2.50e+03 pdb="HH12 ARG B 304 " -0.239 2.00e-02 2.50e+03 pdb="HH21 ARG B 304 " 0.142 2.00e-02 2.50e+03 pdb="HH22 ARG B 304 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 291 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL D 291 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 291 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR D 292 " -0.017 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 882 2.22 - 2.81: 31646 2.81 - 3.41: 37648 3.41 - 4.00: 51753 4.00 - 4.60: 80548 Nonbonded interactions: 202477 Sorted by model distance: nonbonded pdb=" O PHE S 32 " pdb="HH22 ARG S 72 " model vdw 1.623 1.850 nonbonded pdb=" H SER D 265 " pdb=" O ILE D 271 " model vdw 1.650 1.850 nonbonded pdb=" O LYS B 280 " pdb=" HG SER B 281 " model vdw 1.679 1.850 nonbonded pdb="HD22 ASN A 347 " pdb=" O PRO D 221 " model vdw 1.683 1.850 nonbonded pdb="HH22 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 1.726 1.850 ... (remaining 202472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.250 Extract box with map and model: 10.270 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 51.560 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.005 0.061 8410 Z= 0.333 Angle : 0.919 37.125 11461 Z= 0.536 Chirality : 0.049 0.195 1363 Planarity : 0.005 0.126 1444 Dihedral : 14.037 130.178 2779 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.76 % Allowed : 9.24 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.26 (0.25), residues: 1107 helix: 1.99 (0.28), residues: 372 sheet: 0.44 (0.31), residues: 267 loop : -1.56 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 279 HIS 0.005 0.001 HIS B 225 PHE 0.017 0.001 PHE D 379 TYR 0.013 0.001 TYR B 105 ARG 0.006 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.238 Fit side-chains REVERT: B 54 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8228 (m170) REVERT: S 174 GLN cc_start: 0.8289 (tt0) cc_final: 0.8075 (pt0) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 1.5436 time to fit residues: 181.8805 Evaluate side-chains 83 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 13 GLN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8410 Z= 0.157 Angle : 0.481 6.219 11461 Z= 0.256 Chirality : 0.039 0.133 1363 Planarity : 0.003 0.036 1444 Dihedral : 6.530 77.321 1215 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.27 % Allowed : 12.53 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.63 (0.25), residues: 1107 helix: 2.37 (0.28), residues: 382 sheet: 0.59 (0.32), residues: 270 loop : -1.47 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE D 237 TYR 0.011 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.232 Fit side-chains REVERT: B 243 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8390 (m) REVERT: S 174 GLN cc_start: 0.8305 (tt0) cc_final: 0.8095 (pt0) outliers start: 10 outliers final: 4 residues processed: 93 average time/residue: 1.5017 time to fit residues: 154.4016 Evaluate side-chains 82 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8410 Z= 0.179 Angle : 0.488 6.813 11461 Z= 0.261 Chirality : 0.039 0.137 1363 Planarity : 0.003 0.039 1444 Dihedral : 5.826 70.759 1207 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 12.78 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.75 (0.25), residues: 1107 helix: 2.57 (0.28), residues: 381 sheet: 0.65 (0.31), residues: 270 loop : -1.50 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.013 0.001 TYR S 178 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.265 Fit side-chains REVERT: A 14 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 23 LYS cc_start: 0.7482 (ttpt) cc_final: 0.7225 (ttpp) REVERT: B 243 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (m) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 1.5753 time to fit residues: 159.7998 Evaluate side-chains 86 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8410 Z= 0.255 Angle : 0.558 7.487 11461 Z= 0.299 Chirality : 0.041 0.159 1363 Planarity : 0.004 0.045 1444 Dihedral : 5.646 60.786 1207 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.53 % Allowed : 13.80 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.55 (0.25), residues: 1107 helix: 2.41 (0.27), residues: 380 sheet: 0.65 (0.31), residues: 266 loop : -1.66 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.008 0.001 HIS S 35 PHE 0.014 0.002 PHE B 151 TYR 0.017 0.002 TYR S 178 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.283 Fit side-chains REVERT: B 23 LYS cc_start: 0.7545 (ttpt) cc_final: 0.7285 (ttpp) REVERT: B 79 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 243 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8443 (m) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 1.5643 time to fit residues: 165.5322 Evaluate side-chains 90 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8410 Z= 0.272 Angle : 0.568 7.376 11461 Z= 0.305 Chirality : 0.041 0.167 1363 Planarity : 0.004 0.047 1444 Dihedral : 5.428 53.682 1207 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.53 % Allowed : 14.81 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.41 (0.25), residues: 1107 helix: 2.24 (0.27), residues: 382 sheet: 0.63 (0.32), residues: 260 loop : -1.73 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.007 0.001 HIS S 35 PHE 0.016 0.002 PHE D 237 TYR 0.016 0.002 TYR S 178 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 1.281 Fit side-chains REVERT: B 23 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7330 (ttpp) REVERT: B 79 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 243 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8438 (m) REVERT: D 403 ASP cc_start: 0.5204 (OUTLIER) cc_final: 0.4933 (t0) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 1.7778 time to fit residues: 187.4012 Evaluate side-chains 95 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8410 Z= 0.188 Angle : 0.507 6.641 11461 Z= 0.271 Chirality : 0.040 0.146 1363 Planarity : 0.003 0.045 1444 Dihedral : 5.122 49.552 1207 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 15.19 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.62 (0.25), residues: 1107 helix: 2.50 (0.27), residues: 381 sheet: 0.75 (0.31), residues: 267 loop : -1.71 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE D 237 TYR 0.012 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.236 Fit side-chains REVERT: B 23 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7305 (ttpp) REVERT: B 79 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8483 (mp) REVERT: B 243 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8408 (m) REVERT: D 403 ASP cc_start: 0.5222 (m-30) cc_final: 0.4962 (t0) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 1.6024 time to fit residues: 165.4786 Evaluate side-chains 93 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 106 optimal weight: 0.0050 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8410 Z= 0.142 Angle : 0.466 6.723 11461 Z= 0.249 Chirality : 0.039 0.139 1363 Planarity : 0.003 0.041 1444 Dihedral : 4.809 47.407 1207 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.03 % Allowed : 16.08 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.84 (0.25), residues: 1107 helix: 2.79 (0.27), residues: 381 sheet: 0.79 (0.31), residues: 267 loop : -1.65 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE D 237 TYR 0.010 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.375 Fit side-chains REVERT: B 23 LYS cc_start: 0.7501 (ttpt) cc_final: 0.7274 (ttpp) REVERT: B 243 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8390 (m) REVERT: C 29 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7893 (mmtm) REVERT: D 403 ASP cc_start: 0.5349 (m-30) cc_final: 0.5085 (t0) outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 1.6398 time to fit residues: 169.6660 Evaluate side-chains 90 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8410 Z= 0.168 Angle : 0.483 6.667 11461 Z= 0.257 Chirality : 0.039 0.138 1363 Planarity : 0.003 0.040 1444 Dihedral : 4.801 46.550 1207 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.15 % Allowed : 16.20 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.87 (0.25), residues: 1107 helix: 2.83 (0.27), residues: 381 sheet: 0.79 (0.31), residues: 267 loop : -1.63 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.013 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.175 Fit side-chains REVERT: B 23 LYS cc_start: 0.7506 (ttpt) cc_final: 0.7279 (ttpp) REVERT: B 79 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 243 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8396 (m) REVERT: C 29 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7933 (mmtm) REVERT: D 403 ASP cc_start: 0.5332 (m-30) cc_final: 0.5102 (t0) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 1.6255 time to fit residues: 164.6048 Evaluate side-chains 89 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8410 Z= 0.120 Angle : 0.444 6.751 11461 Z= 0.236 Chirality : 0.039 0.139 1363 Planarity : 0.003 0.036 1444 Dihedral : 4.534 45.404 1207 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.65 % Allowed : 16.84 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.06 (0.25), residues: 1107 helix: 3.07 (0.27), residues: 381 sheet: 0.75 (0.31), residues: 269 loop : -1.51 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE B 199 TYR 0.008 0.001 TYR B 124 ARG 0.001 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.359 Fit side-chains REVERT: B 23 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7267 (ttpp) REVERT: B 79 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 243 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8387 (m) REVERT: C 29 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7852 (mmtm) REVERT: D 403 ASP cc_start: 0.5348 (m-30) cc_final: 0.5130 (t0) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 1.6410 time to fit residues: 160.5564 Evaluate side-chains 85 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8410 Z= 0.169 Angle : 0.480 6.703 11461 Z= 0.256 Chirality : 0.039 0.137 1363 Planarity : 0.003 0.037 1444 Dihedral : 4.666 44.943 1207 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.39 % Allowed : 17.22 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.04 (0.25), residues: 1107 helix: 3.02 (0.27), residues: 382 sheet: 0.76 (0.31), residues: 269 loop : -1.52 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.378 Fit side-chains REVERT: B 23 LYS cc_start: 0.7581 (ttpt) cc_final: 0.7358 (ttpp) REVERT: B 243 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8395 (m) REVERT: D 403 ASP cc_start: 0.5330 (m-30) cc_final: 0.5103 (t0) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 1.6901 time to fit residues: 163.2768 Evaluate side-chains 87 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126067 restraints weight = 27573.499| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.93 r_work: 0.3325 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8410 Z= 0.288 Angle : 0.585 7.796 11461 Z= 0.314 Chirality : 0.042 0.175 1363 Planarity : 0.004 0.043 1444 Dihedral : 5.220 49.021 1207 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.65 % Allowed : 16.84 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.72 (0.25), residues: 1107 helix: 2.59 (0.27), residues: 383 sheet: 0.69 (0.31), residues: 266 loop : -1.61 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.008 0.001 HIS S 35 PHE 0.016 0.002 PHE B 151 TYR 0.019 0.002 TYR S 178 ARG 0.003 0.000 ARG B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4967.04 seconds wall clock time: 88 minutes 24.21 seconds (5304.21 seconds total)