Starting phenix.real_space_refine on Fri Feb 16 12:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crh_30452/02_2024/7crh_30452_neut_updated.pdb" } resolution = 3.3 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= -0.028 sd= 0.458 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 7235 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 53 5.16 5 Cl 1 4.86 5 C 5128 2.51 5 N 1402 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" 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: 8068 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2167 Unusual residues: {'GBU': 1} Classifications: {'peptide': 273, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 263, None: 1} Not linked: pdbres="LEU R 344 " pdbres="GBU R 501 " Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.65, per 1000 atoms: 0.58 Number of scatterers: 8068 At special positions: 0 Unit cell: (82.45, 100.3, 130.05, 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) Cl 1 17.00 S 53 16.00 O 1484 8.00 N 1402 7.00 C 5128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.41 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 11 sheets defined 37.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.545A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'R' and resid 21 through 50 removed outlier: 3.661A pdb=" N LEU R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA R 27 " --> pdb=" O ARG R 23 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS R 28 " --> pdb=" O ILE R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 76 removed outlier: 3.692A pdb=" N PHE R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU R 76 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.750A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 123 removed outlier: 3.652A pdb=" N ALA R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 161 removed outlier: 3.698A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.752A pdb=" N LEU R 161 " --> pdb=" O ILE R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 202 removed outlier: 4.337A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 236 removed outlier: 3.569A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 294 removed outlier: 4.392A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.196A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 331 removed outlier: 3.665A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 342 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.121A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.183A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 121 through 123 Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.788A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.848A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.772A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.718A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.908A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 165 through 170 removed outlier: 3.717A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.514A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 969 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: 2.52 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2627 1.35 - 1.46: 2032 1.46 - 1.58: 3504 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8236 Sorted by residual: bond pdb=" C01 GBU R 501 " pdb=" N02 GBU R 501 " ideal model delta sigma weight residual 1.538 1.279 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C10 GBU R 501 " pdb=" O11 GBU R 501 " ideal model delta sigma weight residual 1.379 1.481 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C08 GBU R 501 " pdb=" C10 GBU R 501 " ideal model delta sigma weight residual 1.421 1.331 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C15 GBU R 501 " pdb=" N02 GBU R 501 " ideal model delta sigma weight residual 1.479 1.399 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C18 GBU R 501 " pdb=" C19 GBU R 501 " ideal model delta sigma weight residual 1.537 1.466 0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 8231 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.30: 220 107.30 - 113.98: 4632 113.98 - 120.66: 3344 120.66 - 127.34: 2888 127.34 - 134.02: 89 Bond angle restraints: 11173 Sorted by residual: angle pdb=" N GLY A 355 " pdb=" CA GLY A 355 " pdb=" C GLY A 355 " ideal model delta sigma weight residual 115.30 110.39 4.91 1.39e+00 5.18e-01 1.25e+01 angle pdb=" C04 GBU R 501 " pdb=" C05 GBU R 501 " pdb=" C06 GBU R 501 " ideal model delta sigma weight residual 110.99 121.43 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ASN R 292 " pdb=" CA ASN R 292 " pdb=" C ASN R 292 " ideal model delta sigma weight residual 113.01 109.12 3.89 1.20e+00 6.94e-01 1.05e+01 angle pdb=" C05 GBU R 501 " pdb=" C06 GBU R 501 " pdb=" C14 GBU R 501 " ideal model delta sigma weight residual 110.68 120.30 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 110.27 3.20 1.01e+00 9.80e-01 1.00e+01 ... (remaining 11168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 4739 32.39 - 64.78: 135 64.78 - 97.17: 10 97.17 - 129.56: 0 129.56 - 161.95: 1 Dihedral angle restraints: 4885 sinusoidal: 1869 harmonic: 3016 Sorted by residual: dihedral pdb=" C05 GBU R 501 " pdb=" C03 GBU R 501 " pdb=" C04 GBU R 501 " pdb=" N02 GBU R 501 " ideal model delta sinusoidal sigma weight residual 79.31 -82.64 161.95 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -124.42 38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CA SER R 162 " pdb=" C SER R 162 " pdb=" N TRP R 163 " pdb=" CA TRP R 163 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 4882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 808 0.030 - 0.060: 308 0.060 - 0.090: 96 0.090 - 0.121: 51 0.121 - 0.151: 8 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CB THR R 42 " pdb=" CA THR R 42 " pdb=" OG1 THR R 42 " pdb=" CG2 THR R 42 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA VAL B 100 " pdb=" N VAL B 100 " pdb=" C VAL B 100 " pdb=" CB VAL B 100 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1268 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 136 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO R 137 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 137 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 137 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 327 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO R 328 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 328 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 328 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 117 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C ILE R 117 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 117 " -0.010 2.00e-02 2.50e+03 pdb=" N SER R 118 " -0.009 2.00e-02 2.50e+03 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 20 2.42 - 3.04: 4891 3.04 - 3.66: 12265 3.66 - 4.28: 17094 4.28 - 4.90: 28577 Nonbonded interactions: 62847 Sorted by model distance: nonbonded pdb=" NH2 ARG A 232 " pdb=" SG CYS B 204 " model vdw 1.798 2.880 nonbonded pdb=" O TYR B 59 " pdb=" SG CYS B 317 " model vdw 1.925 3.400 nonbonded pdb=" O ASP B 290 " pdb=" OD1 ASP B 290 " model vdw 2.121 3.040 nonbonded pdb=" O ALA R 322 " pdb=" OG SER R 325 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.238 2.440 ... (remaining 62842 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.860 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.004 0.259 8236 Z= 0.278 Angle : 0.587 10.443 11173 Z= 0.351 Chirality : 0.040 0.151 1271 Planarity : 0.003 0.041 1417 Dihedral : 14.338 161.948 2913 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.40 % Allowed : 23.31 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1015 helix: -1.18 (0.23), residues: 406 sheet: -1.48 (0.32), residues: 210 loop : -2.62 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.001 0.000 HIS B 311 PHE 0.007 0.001 PHE R 297 TYR 0.006 0.001 TYR B 59 ARG 0.002 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 297 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 284 THR cc_start: 0.9315 (p) cc_final: 0.9071 (t) REVERT: A 309 GLU cc_start: 0.7794 (tp30) cc_final: 0.6890 (mt-10) REVERT: A 317 ARG cc_start: 0.7886 (mmp-170) cc_final: 0.7286 (mtm-85) REVERT: B 32 GLN cc_start: 0.7103 (pt0) cc_final: 0.6708 (tp-100) REVERT: G 20 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8258 (tppt) REVERT: N 69 THR cc_start: 0.7474 (p) cc_final: 0.7232 (p) REVERT: R 61 PHE cc_start: 0.7811 (m-80) cc_final: 0.7601 (m-10) REVERT: R 118 SER cc_start: 0.9172 (m) cc_final: 0.8906 (p) REVERT: R 157 ILE cc_start: 0.8373 (mt) cc_final: 0.8145 (mp) REVERT: R 268 THR cc_start: 0.8352 (p) cc_final: 0.8052 (t) REVERT: R 290 ILE cc_start: 0.9350 (tp) cc_final: 0.9144 (tp) outliers start: 12 outliers final: 6 residues processed: 305 average time/residue: 0.1999 time to fit residues: 81.5925 Evaluate side-chains 205 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain R residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 384 GLN B 175 GLN B 230 ASN N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8236 Z= 0.226 Angle : 0.634 10.228 11173 Z= 0.321 Chirality : 0.042 0.175 1271 Planarity : 0.004 0.049 1417 Dihedral : 8.226 162.422 1137 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.41 % Allowed : 22.84 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1015 helix: 0.25 (0.25), residues: 399 sheet: -1.06 (0.34), residues: 206 loop : -2.13 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.013 0.002 HIS B 225 PHE 0.022 0.002 PHE R 289 TYR 0.016 0.002 TYR B 145 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 215 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 317 ARG cc_start: 0.7758 (mmp-170) cc_final: 0.7262 (mtm-85) REVERT: R 25 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7973 (pp) REVERT: R 61 PHE cc_start: 0.8060 (m-80) cc_final: 0.7827 (m-10) REVERT: R 118 SER cc_start: 0.9145 (m) cc_final: 0.8813 (p) REVERT: R 157 ILE cc_start: 0.8447 (mt) cc_final: 0.8243 (mp) REVERT: R 290 ILE cc_start: 0.9403 (tp) cc_final: 0.9196 (tp) REVERT: R 333 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7858 (t80) outliers start: 55 outliers final: 33 residues processed: 254 average time/residue: 0.1724 time to fit residues: 61.0174 Evaluate side-chains 223 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 271 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN N 31 ASN R 185 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8236 Z= 0.263 Angle : 0.613 9.098 11173 Z= 0.318 Chirality : 0.042 0.162 1271 Planarity : 0.004 0.050 1417 Dihedral : 8.182 164.303 1131 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 8.28 % Allowed : 23.31 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1015 helix: 0.50 (0.26), residues: 405 sheet: -1.03 (0.34), residues: 202 loop : -2.05 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.007 0.001 HIS B 225 PHE 0.017 0.001 PHE R 203 TYR 0.012 0.002 TYR N 115 ARG 0.004 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 190 time to evaluate : 0.953 Fit side-chains REVERT: A 309 GLU cc_start: 0.7384 (tp30) cc_final: 0.6038 (mt-10) REVERT: A 327 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5750 (mp0) REVERT: B 189 SER cc_start: 0.8955 (t) cc_final: 0.8683 (p) REVERT: N 64 VAL cc_start: 0.8699 (t) cc_final: 0.8230 (p) REVERT: N 108 PHE cc_start: 0.3049 (OUTLIER) cc_final: 0.1526 (p90) REVERT: N 109 ASP cc_start: 0.7150 (m-30) cc_final: 0.6852 (m-30) REVERT: R 25 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7944 (pp) REVERT: R 61 PHE cc_start: 0.8173 (m-80) cc_final: 0.7954 (m-10) REVERT: R 104 ILE cc_start: 0.8823 (pt) cc_final: 0.8588 (tt) REVERT: R 118 SER cc_start: 0.9252 (m) cc_final: 0.8921 (p) REVERT: R 157 ILE cc_start: 0.8528 (mt) cc_final: 0.8327 (mp) REVERT: R 290 ILE cc_start: 0.9391 (tp) cc_final: 0.9186 (tp) REVERT: R 339 LYS cc_start: 0.8929 (tppt) cc_final: 0.8696 (tppt) REVERT: R 341 PHE cc_start: 0.7145 (t80) cc_final: 0.6856 (t80) outliers start: 71 outliers final: 48 residues processed: 240 average time/residue: 0.1719 time to fit residues: 58.3075 Evaluate side-chains 232 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 26 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN B 237 ASN N 31 ASN N 39 GLN N 53 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8236 Z= 0.262 Angle : 0.624 9.880 11173 Z= 0.322 Chirality : 0.043 0.146 1271 Planarity : 0.004 0.047 1417 Dihedral : 8.279 164.076 1131 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 8.16 % Allowed : 24.94 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.26), residues: 1015 helix: 0.51 (0.26), residues: 410 sheet: -0.99 (0.34), residues: 201 loop : -2.13 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.008 0.001 HIS B 225 PHE 0.015 0.001 PHE N 68 TYR 0.014 0.001 TYR A 358 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 199 time to evaluate : 0.914 Fit side-chains REVERT: A 216 LYS cc_start: 0.9091 (mppt) cc_final: 0.8854 (mmtt) REVERT: A 309 GLU cc_start: 0.7569 (tp30) cc_final: 0.6249 (mt-10) REVERT: A 327 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: B 75 GLN cc_start: 0.8310 (mt0) cc_final: 0.8027 (mt0) REVERT: G 19 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8316 (mp) REVERT: N 108 PHE cc_start: 0.3431 (OUTLIER) cc_final: 0.1898 (p90) REVERT: R 61 PHE cc_start: 0.8221 (m-80) cc_final: 0.7939 (m-10) REVERT: R 78 MET cc_start: 0.8346 (tpp) cc_final: 0.7901 (tpp) REVERT: R 104 ILE cc_start: 0.8811 (pt) cc_final: 0.8569 (tt) REVERT: R 118 SER cc_start: 0.9250 (m) cc_final: 0.8924 (p) REVERT: R 157 ILE cc_start: 0.8617 (mt) cc_final: 0.8411 (mp) REVERT: R 339 LYS cc_start: 0.8944 (tppt) cc_final: 0.8699 (tppt) REVERT: R 341 PHE cc_start: 0.7035 (t80) cc_final: 0.6584 (t80) outliers start: 70 outliers final: 50 residues processed: 247 average time/residue: 0.1608 time to fit residues: 56.7039 Evaluate side-chains 234 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 181 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.0570 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.0040 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 overall best weight: 0.2848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 384 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 340 ASN N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8236 Z= 0.165 Angle : 0.587 10.606 11173 Z= 0.299 Chirality : 0.041 0.191 1271 Planarity : 0.003 0.048 1417 Dihedral : 8.132 165.397 1131 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.13 % Allowed : 28.55 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1015 helix: 0.77 (0.26), residues: 406 sheet: -0.76 (0.35), residues: 197 loop : -2.01 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.001 PHE N 103 TYR 0.012 0.001 TYR G 40 ARG 0.003 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 0.978 Fit side-chains REVERT: A 255 MET cc_start: 0.2838 (pmm) cc_final: 0.1291 (pmm) REVERT: A 309 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6130 (mt-10) REVERT: A 327 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5896 (mp0) REVERT: G 19 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8255 (mp) REVERT: N 39 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7658 (pp30) REVERT: N 108 PHE cc_start: 0.2862 (OUTLIER) cc_final: 0.1507 (p90) REVERT: R 20 PHE cc_start: 0.4418 (OUTLIER) cc_final: 0.3079 (m-80) REVERT: R 104 ILE cc_start: 0.8801 (pt) cc_final: 0.8601 (tt) REVERT: R 118 SER cc_start: 0.9201 (m) cc_final: 0.8844 (p) REVERT: R 157 ILE cc_start: 0.8648 (mt) cc_final: 0.8445 (mp) REVERT: R 339 LYS cc_start: 0.8973 (tppt) cc_final: 0.8707 (tppt) REVERT: R 341 PHE cc_start: 0.7019 (t80) cc_final: 0.6491 (t80) outliers start: 44 outliers final: 25 residues processed: 249 average time/residue: 0.1619 time to fit residues: 57.2424 Evaluate side-chains 223 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8236 Z= 0.247 Angle : 0.614 8.940 11173 Z= 0.317 Chirality : 0.043 0.191 1271 Planarity : 0.004 0.047 1417 Dihedral : 8.267 164.238 1131 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.29 % Allowed : 28.21 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1015 helix: 0.85 (0.26), residues: 407 sheet: -0.74 (0.36), residues: 199 loop : -1.96 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.005 0.001 HIS B 225 PHE 0.009 0.001 PHE B 292 TYR 0.013 0.001 TYR G 40 ARG 0.002 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 195 time to evaluate : 0.927 Fit side-chains REVERT: A 255 MET cc_start: 0.3132 (pmm) cc_final: 0.2891 (pmm) REVERT: A 309 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: A 327 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: N 108 PHE cc_start: 0.3241 (OUTLIER) cc_final: 0.1744 (p90) REVERT: R 118 SER cc_start: 0.9219 (m) cc_final: 0.8913 (p) REVERT: R 157 ILE cc_start: 0.8664 (mt) cc_final: 0.8462 (mp) REVERT: R 339 LYS cc_start: 0.8983 (tppt) cc_final: 0.8720 (tppt) REVERT: R 341 PHE cc_start: 0.7071 (t80) cc_final: 0.6449 (t80) outliers start: 54 outliers final: 44 residues processed: 230 average time/residue: 0.1580 time to fit residues: 51.6811 Evaluate side-chains 239 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 192 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8236 Z= 0.177 Angle : 0.613 12.098 11173 Z= 0.310 Chirality : 0.042 0.183 1271 Planarity : 0.003 0.047 1417 Dihedral : 8.193 163.757 1131 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.18 % Allowed : 29.60 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1015 helix: 0.91 (0.26), residues: 407 sheet: -0.62 (0.36), residues: 199 loop : -1.92 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 292 TYR 0.011 0.001 TYR G 40 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 0.950 Fit side-chains REVERT: A 255 MET cc_start: 0.3221 (pmm) cc_final: 0.2964 (pmm) REVERT: A 309 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6200 (mt-10) REVERT: A 327 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: B 32 GLN cc_start: 0.7100 (pt0) cc_final: 0.6611 (tp-100) REVERT: N 39 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7575 (pp30) REVERT: N 108 PHE cc_start: 0.3101 (OUTLIER) cc_final: 0.1645 (p90) REVERT: R 20 PHE cc_start: 0.4584 (OUTLIER) cc_final: 0.3289 (m-80) REVERT: R 118 SER cc_start: 0.9199 (m) cc_final: 0.8894 (p) REVERT: R 157 ILE cc_start: 0.8693 (mt) cc_final: 0.8493 (mp) REVERT: R 339 LYS cc_start: 0.8975 (tppt) cc_final: 0.8702 (tppt) REVERT: R 341 PHE cc_start: 0.7005 (t80) cc_final: 0.6387 (t80) outliers start: 53 outliers final: 39 residues processed: 236 average time/residue: 0.1589 time to fit residues: 53.5457 Evaluate side-chains 234 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8236 Z= 0.214 Angle : 0.628 12.979 11173 Z= 0.316 Chirality : 0.042 0.210 1271 Planarity : 0.004 0.047 1417 Dihedral : 8.191 163.227 1131 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.11 % Allowed : 28.79 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 1015 helix: 0.95 (0.26), residues: 407 sheet: -0.59 (0.36), residues: 199 loop : -1.94 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE N 68 TYR 0.011 0.001 TYR G 40 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 0.898 Fit side-chains REVERT: A 255 MET cc_start: 0.3373 (pmm) cc_final: 0.3087 (pmm) REVERT: A 309 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6327 (mt-10) REVERT: A 327 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: N 108 PHE cc_start: 0.3247 (OUTLIER) cc_final: 0.1759 (p90) REVERT: R 20 PHE cc_start: 0.4572 (OUTLIER) cc_final: 0.3326 (m-80) REVERT: R 118 SER cc_start: 0.9211 (m) cc_final: 0.8907 (p) REVERT: R 157 ILE cc_start: 0.8690 (mt) cc_final: 0.8483 (mp) REVERT: R 339 LYS cc_start: 0.8995 (tppt) cc_final: 0.8715 (tppt) outliers start: 61 outliers final: 48 residues processed: 229 average time/residue: 0.1616 time to fit residues: 52.9525 Evaluate side-chains 237 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8236 Z= 0.315 Angle : 0.696 14.050 11173 Z= 0.352 Chirality : 0.044 0.213 1271 Planarity : 0.004 0.043 1417 Dihedral : 8.295 162.793 1130 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 6.76 % Allowed : 29.95 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1015 helix: 0.84 (0.26), residues: 406 sheet: -0.67 (0.36), residues: 198 loop : -2.00 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.001 PHE N 68 TYR 0.017 0.002 TYR G 40 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 183 time to evaluate : 1.010 Fit side-chains REVERT: A 255 MET cc_start: 0.3475 (pmm) cc_final: 0.3178 (pmm) REVERT: A 309 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6349 (mt-10) REVERT: A 327 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: N 39 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7628 (pp30) REVERT: N 108 PHE cc_start: 0.3454 (OUTLIER) cc_final: 0.1956 (p90) REVERT: R 20 PHE cc_start: 0.4674 (OUTLIER) cc_final: 0.3567 (m-80) REVERT: R 57 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8132 (mmtp) REVERT: R 118 SER cc_start: 0.9254 (m) cc_final: 0.8923 (p) REVERT: R 157 ILE cc_start: 0.8680 (mt) cc_final: 0.8456 (mp) REVERT: R 339 LYS cc_start: 0.8989 (tppt) cc_final: 0.8709 (tppt) outliers start: 58 outliers final: 47 residues processed: 225 average time/residue: 0.1549 time to fit residues: 50.4517 Evaluate side-chains 231 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 179 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 0.0030 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8236 Z= 0.181 Angle : 0.648 14.657 11173 Z= 0.322 Chirality : 0.042 0.206 1271 Planarity : 0.003 0.044 1417 Dihedral : 8.211 164.093 1130 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.06 % Allowed : 30.54 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 1015 helix: 0.95 (0.27), residues: 402 sheet: -0.50 (0.36), residues: 198 loop : -1.91 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.023 0.001 PHE N 68 TYR 0.013 0.001 TYR G 40 ARG 0.002 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.031 Fit side-chains REVERT: A 255 MET cc_start: 0.3625 (pmm) cc_final: 0.3363 (pmm) REVERT: A 309 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6329 (mt-10) REVERT: A 327 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: B 219 ARG cc_start: 0.8277 (mmt180) cc_final: 0.8027 (mmm160) REVERT: N 108 PHE cc_start: 0.3197 (OUTLIER) cc_final: 0.1758 (p90) REVERT: R 20 PHE cc_start: 0.4671 (OUTLIER) cc_final: 0.3536 (m-80) REVERT: R 118 SER cc_start: 0.9227 (m) cc_final: 0.8933 (p) REVERT: R 157 ILE cc_start: 0.8708 (mt) cc_final: 0.8485 (mp) REVERT: R 339 LYS cc_start: 0.9026 (tppt) cc_final: 0.8745 (tppt) outliers start: 52 outliers final: 43 residues processed: 226 average time/residue: 0.1676 time to fit residues: 53.6702 Evaluate side-chains 229 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094385 restraints weight = 20751.444| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.21 r_work: 0.3332 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8236 Z= 0.284 Angle : 0.704 14.803 11173 Z= 0.351 Chirality : 0.044 0.214 1271 Planarity : 0.004 0.043 1417 Dihedral : 8.272 162.913 1130 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.83 % Allowed : 30.89 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 1015 helix: 0.87 (0.27), residues: 402 sheet: -0.46 (0.37), residues: 195 loop : -1.90 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.022 0.001 PHE N 68 TYR 0.016 0.001 TYR G 40 ARG 0.002 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.31 seconds wall clock time: 37 minutes 49.14 seconds (2269.14 seconds total)