Starting phenix.real_space_refine on Wed Feb 14 08:04:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td4_25823/02_2024/7td4_25823_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.981 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 2031 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 51 5.16 5 C 4417 2.51 5 N 1159 2.21 5 O 1263 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 27": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ASP 91": "OD1" <-> "OD2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R ARG 229": "NH1" <-> "NH2" Residue "R ARG 231": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6893 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2497 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 368 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2271 Unusual residues: {'J8C': 1, 'NAG': 1} Classifications: {'peptide': 290, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 283, None: 2} Not linked: pdbres="ILE R 323 " pdbres="NAG R 401 " Not linked: pdbres="NAG R 401 " pdbres="J8C R 402 " Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 3.88, per 1000 atoms: 0.56 Number of scatterers: 6893 At special positions: 0 Unit cell: (92.568, 94.696, 129.808, 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 51 16.00 F 3 9.00 O 1263 8.00 N 1159 7.00 C 4417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 191 " distance=1.81 Simple disulfide: pdb=" SG CYS R 282 " - pdb=" SG CYS R 287 " distance=2.02 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 Links applied NAG-ASN " NAG R 401 " - " ASN R 30 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 40.6% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.870A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.730A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.722A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 22 through 32 removed outlier: 3.929A pdb=" N VAL R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 72 Processing helix chain 'R' and resid 79 through 103 Processing helix chain 'R' and resid 106 through 108 No H-bonds generated for 'chain 'R' and resid 106 through 108' Processing helix chain 'R' and resid 114 through 148 removed outlier: 3.786A pdb=" N MET R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 176 removed outlier: 3.884A pdb=" N TRP R 168 " --> pdb=" O ILE R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 233 Processing helix chain 'R' and resid 249 through 281 removed outlier: 3.669A pdb=" N ALA R 253 " --> pdb=" O GLU R 249 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 289 through 291 No H-bonds generated for 'chain 'R' and resid 289 through 291' Processing helix chain 'R' and resid 294 through 313 removed outlier: 4.038A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY R 305 " --> pdb=" O VAL R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 318 through 322 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.891A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.732A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.003A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.508A 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: 6.808A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.843A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.627A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.369A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 957 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: 1.86 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1108 1.29 - 1.42: 1837 1.42 - 1.56: 4011 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 7028 Sorted by residual: bond pdb=" C16 J8C R 402 " pdb=" C19 J8C R 402 " ideal model delta sigma weight residual 0.000 1.521 -1.521 2.00e-02 2.50e+03 5.79e+03 bond pdb=" C12 J8C R 402 " pdb=" C13 J8C R 402 " ideal model delta sigma weight residual 1.958 1.499 0.459 2.00e-02 2.50e+03 5.27e+02 bond pdb=" C25 J8C R 402 " pdb=" F28 J8C R 402 " ideal model delta sigma weight residual 1.506 1.318 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C35 J8C R 402 " pdb=" O37 J8C R 402 " ideal model delta sigma weight residual 1.378 1.212 0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C16 J8C R 402 " pdb=" C17 J8C R 402 " ideal model delta sigma weight residual 1.524 1.388 0.136 2.00e-02 2.50e+03 4.59e+01 ... (remaining 7023 not shown) Histogram of bond angle deviations from ideal: 85.07 - 94.86: 4 94.86 - 104.64: 67 104.64 - 114.43: 4269 114.43 - 124.22: 5041 124.22 - 134.01: 165 Bond angle restraints: 9546 Sorted by residual: angle pdb=" C GLU R 141 " pdb=" CA GLU R 141 " pdb=" CB GLU R 141 " ideal model delta sigma weight residual 110.88 101.03 9.85 1.57e+00 4.06e-01 3.94e+01 angle pdb=" C HIS R 152 " pdb=" N ASN R 153 " pdb=" CA ASN R 153 " ideal model delta sigma weight residual 122.77 115.03 7.74 1.33e+00 5.65e-01 3.38e+01 angle pdb=" CA THR R 193 " pdb=" CB THR R 193 " pdb=" OG1 THR R 193 " ideal model delta sigma weight residual 109.60 101.33 8.27 1.50e+00 4.44e-01 3.04e+01 angle pdb=" CA VAL R 194 " pdb=" C VAL R 194 " pdb=" O VAL R 194 " ideal model delta sigma weight residual 121.29 115.41 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" C12 J8C R 402 " pdb=" C13 J8C R 402 " pdb=" C14 J8C R 402 " ideal model delta sigma weight residual 105.15 121.51 -16.36 3.00e+00 1.11e-01 2.97e+01 ... (remaining 9541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 3758 13.82 - 27.65: 311 27.65 - 41.47: 62 41.47 - 55.29: 19 55.29 - 69.11: 11 Dihedral angle restraints: 4161 sinusoidal: 1550 harmonic: 2611 Sorted by residual: dihedral pdb=" C GLU R 141 " pdb=" N GLU R 141 " pdb=" CA GLU R 141 " pdb=" CB GLU R 141 " ideal model delta harmonic sigma weight residual -122.60 -110.37 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ASP A 350 " pdb=" C ASP A 350 " pdb=" N CYS A 351 " pdb=" CA CYS A 351 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C HIS R 77 " pdb=" N HIS R 77 " pdb=" CA HIS R 77 " pdb=" CB HIS R 77 " ideal model delta harmonic sigma weight residual -122.60 -132.65 10.05 0 2.50e+00 1.60e-01 1.62e+01 ... (remaining 4158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.128: 1126 1.128 - 2.256: 0 2.256 - 3.385: 0 3.385 - 4.513: 0 4.513 - 5.641: 1 Chirality restraints: 1127 Sorted by residual: chirality pdb=" C33 J8C R 402 " pdb=" C32 J8C R 402 " pdb=" C34 J8C R 402 " pdb=" C35 J8C R 402 " both_signs ideal model delta sigma weight residual False -2.82 2.82 -5.64 2.00e-01 2.50e+01 7.96e+02 chirality pdb=" CA TYR R 81 " pdb=" N TYR R 81 " pdb=" C TYR R 81 " pdb=" CB TYR R 81 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA GLU R 141 " pdb=" N GLU R 141 " pdb=" C GLU R 141 " pdb=" CB GLU R 141 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1124 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 J8C R 402 " 0.092 2.00e-02 2.50e+03 5.30e-02 6.33e+01 pdb=" C13 J8C R 402 " -0.017 2.00e-02 2.50e+03 pdb=" C14 J8C R 402 " -0.022 2.00e-02 2.50e+03 pdb=" C15 J8C R 402 " -0.019 2.00e-02 2.50e+03 pdb=" C16 J8C R 402 " -0.017 2.00e-02 2.50e+03 pdb=" C17 J8C R 402 " -0.051 2.00e-02 2.50e+03 pdb=" C18 J8C R 402 " -0.045 2.00e-02 2.50e+03 pdb=" C19 J8C R 402 " 0.102 2.00e-02 2.50e+03 pdb=" C25 J8C R 402 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 J8C R 402 " -0.042 2.00e-02 2.50e+03 3.22e-02 2.33e+01 pdb=" C03 J8C R 402 " 0.037 2.00e-02 2.50e+03 pdb=" C04 J8C R 402 " 0.023 2.00e-02 2.50e+03 pdb=" C05 J8C R 402 " 0.006 2.00e-02 2.50e+03 pdb=" C06 J8C R 402 " -0.009 2.00e-02 2.50e+03 pdb=" C07 J8C R 402 " 0.012 2.00e-02 2.50e+03 pdb=" C08 J8C R 402 " 0.049 2.00e-02 2.50e+03 pdb=" C09 J8C R 402 " -0.046 2.00e-02 2.50e+03 pdb=" C30 J8C R 402 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 151 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C LEU R 151 " 0.073 2.00e-02 2.50e+03 pdb=" O LEU R 151 " -0.027 2.00e-02 2.50e+03 pdb=" N HIS R 152 " -0.025 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 190 2.70 - 3.25: 6944 3.25 - 3.80: 11045 3.80 - 4.35: 14769 4.35 - 4.90: 24438 Nonbonded interactions: 57386 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.200 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.340 2.440 nonbonded pdb=" O LEU R 177 " pdb=" O GLY R 181 " model vdw 2.371 3.040 ... (remaining 57381 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 3.730 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.000 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.021 1.521 7028 Z= 1.609 Angle : 0.824 16.358 9546 Z= 0.505 Chirality : 0.175 5.641 1127 Planarity : 0.005 0.053 1188 Dihedral : 11.652 69.114 2461 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.84 % Allowed : 5.87 % Favored : 93.30 % Cbeta Deviations : 0.35 % 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: 0.11 (0.28), residues: 880 helix: 1.26 (0.27), residues: 367 sheet: 0.27 (0.41), residues: 178 loop : -1.37 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.012 0.001 HIS R 152 PHE 0.020 0.002 PHE R 83 TYR 0.027 0.002 TYR R 82 ARG 0.005 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8677 (m-40) cc_final: 0.8442 (m-40) REVERT: A 22 ASN cc_start: 0.8394 (m-40) cc_final: 0.8192 (m110) REVERT: A 24 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7115 (ttm110) REVERT: R 48 THR cc_start: 0.7502 (p) cc_final: 0.7259 (m) REVERT: R 146 MET cc_start: 0.8835 (mmm) cc_final: 0.8579 (tpp) REVERT: R 229 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.6948 (ttt90) outliers start: 6 outliers final: 3 residues processed: 160 average time/residue: 1.0905 time to fit residues: 184.3097 Evaluate side-chains 137 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 164 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.0470 chunk 80 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN R 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7028 Z= 0.213 Angle : 0.574 11.318 9546 Z= 0.291 Chirality : 0.041 0.151 1127 Planarity : 0.004 0.049 1188 Dihedral : 6.122 61.178 999 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.65 % Allowed : 11.03 % Favored : 86.31 % 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: 0.61 (0.28), residues: 880 helix: 1.84 (0.27), residues: 359 sheet: 0.41 (0.39), residues: 173 loop : -1.15 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS R 77 PHE 0.024 0.002 PHE R 273 TYR 0.012 0.001 TYR R 98 ARG 0.003 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8632 (m-40) cc_final: 0.8382 (m-40) REVERT: A 24 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7115 (ttm110) REVERT: R 48 THR cc_start: 0.7531 (p) cc_final: 0.7299 (m) REVERT: R 146 MET cc_start: 0.8734 (mmm) cc_final: 0.8524 (tpp) REVERT: R 229 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.6853 (ttt90) outliers start: 19 outliers final: 10 residues processed: 154 average time/residue: 1.0845 time to fit residues: 176.6443 Evaluate side-chains 148 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 7028 Z= 0.257 Angle : 0.560 10.292 9546 Z= 0.287 Chirality : 0.042 0.156 1127 Planarity : 0.004 0.050 1188 Dihedral : 5.774 63.073 995 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.35 % Allowed : 11.87 % Favored : 84.78 % 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: 0.57 (0.28), residues: 880 helix: 1.77 (0.27), residues: 366 sheet: 0.31 (0.39), residues: 177 loop : -1.16 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 PHE 0.020 0.002 PHE R 273 TYR 0.011 0.001 TYR R 98 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8629 (m-40) cc_final: 0.8378 (m-40) REVERT: A 24 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7070 (ttm110) REVERT: R 48 THR cc_start: 0.7537 (p) cc_final: 0.7298 (m) REVERT: R 146 MET cc_start: 0.8814 (mmm) cc_final: 0.8550 (tpp) REVERT: R 229 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.6858 (ttt90) outliers start: 24 outliers final: 18 residues processed: 154 average time/residue: 1.1118 time to fit residues: 180.7753 Evaluate side-chains 153 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 191 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7028 Z= 0.207 Angle : 0.537 12.225 9546 Z= 0.271 Chirality : 0.041 0.150 1127 Planarity : 0.003 0.049 1188 Dihedral : 5.662 65.708 995 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.21 % Allowed : 13.41 % Favored : 83.38 % 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: 0.61 (0.28), residues: 880 helix: 1.87 (0.27), residues: 366 sheet: 0.23 (0.39), residues: 179 loop : -1.15 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.019 0.001 PHE R 273 TYR 0.013 0.001 TYR R 98 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8597 (m-40) cc_final: 0.8356 (m-40) REVERT: A 14 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6936 (mt-10) REVERT: A 24 ARG cc_start: 0.7417 (ttm110) cc_final: 0.7013 (ttm110) REVERT: A 53 MET cc_start: 0.6906 (ttm) cc_final: 0.6671 (ttm) REVERT: R 48 THR cc_start: 0.7532 (p) cc_final: 0.7285 (m) REVERT: R 229 ARG cc_start: 0.7450 (ttp-170) cc_final: 0.6869 (ttt90) outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 1.0279 time to fit residues: 166.5463 Evaluate side-chains 150 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 191 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 7028 Z= 0.217 Angle : 0.534 10.284 9546 Z= 0.270 Chirality : 0.041 0.146 1127 Planarity : 0.003 0.049 1188 Dihedral : 5.612 66.975 995 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.35 % Allowed : 14.11 % Favored : 82.54 % 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: 0.68 (0.28), residues: 880 helix: 1.96 (0.27), residues: 367 sheet: 0.22 (0.38), residues: 179 loop : -1.16 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.018 0.001 PHE R 273 TYR 0.011 0.001 TYR R 98 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8598 (m-40) cc_final: 0.8358 (m-40) REVERT: A 14 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6899 (mt-10) REVERT: A 24 ARG cc_start: 0.7419 (ttm110) cc_final: 0.7012 (ttm110) REVERT: A 53 MET cc_start: 0.6893 (ttm) cc_final: 0.6626 (ttm) REVERT: R 48 THR cc_start: 0.7430 (p) cc_final: 0.7188 (m) REVERT: R 229 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6870 (ttt90) outliers start: 24 outliers final: 16 residues processed: 148 average time/residue: 1.1122 time to fit residues: 173.8294 Evaluate side-chains 155 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 0.0050 chunk 49 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7028 Z= 0.205 Angle : 0.526 10.373 9546 Z= 0.265 Chirality : 0.041 0.160 1127 Planarity : 0.003 0.048 1188 Dihedral : 5.589 68.914 995 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.93 % Allowed : 14.66 % Favored : 82.40 % 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: 0.71 (0.28), residues: 880 helix: 2.00 (0.27), residues: 367 sheet: 0.23 (0.38), residues: 179 loop : -1.15 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE R 273 TYR 0.011 0.001 TYR R 98 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8589 (m-40) cc_final: 0.8345 (m-40) REVERT: A 14 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 24 ARG cc_start: 0.7373 (ttm110) cc_final: 0.6972 (ttm110) REVERT: R 27 ARG cc_start: 0.7301 (ttm110) cc_final: 0.7021 (ttm-80) REVERT: R 48 THR cc_start: 0.7433 (p) cc_final: 0.7173 (m) REVERT: R 229 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.6859 (ttt90) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 1.1317 time to fit residues: 180.7484 Evaluate side-chains 153 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7028 Z= 0.181 Angle : 0.517 10.982 9546 Z= 0.261 Chirality : 0.041 0.193 1127 Planarity : 0.003 0.048 1188 Dihedral : 5.520 70.721 995 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.93 % Allowed : 14.25 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 880 helix: 2.10 (0.27), residues: 367 sheet: 0.23 (0.38), residues: 184 loop : -1.08 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.023 0.001 PHE R 205 TYR 0.011 0.001 TYR R 98 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8575 (m-40) cc_final: 0.8331 (m-40) REVERT: A 14 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 24 ARG cc_start: 0.7367 (ttm110) cc_final: 0.6968 (ttm110) REVERT: R 27 ARG cc_start: 0.7357 (ttm110) cc_final: 0.7027 (ttm-80) REVERT: R 48 THR cc_start: 0.7426 (p) cc_final: 0.7176 (m) REVERT: R 229 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.6864 (ttt90) outliers start: 21 outliers final: 15 residues processed: 149 average time/residue: 1.0765 time to fit residues: 169.8525 Evaluate side-chains 155 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 7028 Z= 0.177 Angle : 0.524 10.512 9546 Z= 0.262 Chirality : 0.041 0.241 1127 Planarity : 0.003 0.048 1188 Dihedral : 5.509 72.000 995 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.79 % Allowed : 14.80 % Favored : 82.40 % 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: 0.85 (0.28), residues: 880 helix: 2.12 (0.27), residues: 367 sheet: 0.28 (0.38), residues: 183 loop : -1.08 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS A 188 PHE 0.017 0.001 PHE R 273 TYR 0.011 0.001 TYR R 98 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7234 (mtp85) cc_final: 0.7023 (mmm-85) REVERT: B 239 ASN cc_start: 0.8564 (m-40) cc_final: 0.8318 (m-40) REVERT: A 24 ARG cc_start: 0.7412 (ttm110) cc_final: 0.7042 (ttm110) REVERT: A 269 ASN cc_start: 0.8371 (m110) cc_final: 0.8138 (m110) REVERT: R 27 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6963 (ttm-80) REVERT: R 48 THR cc_start: 0.7419 (p) cc_final: 0.7203 (m) REVERT: R 92 LEU cc_start: 0.8929 (tp) cc_final: 0.8721 (tm) REVERT: R 229 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.6865 (ttt90) outliers start: 20 outliers final: 15 residues processed: 147 average time/residue: 1.2004 time to fit residues: 186.2289 Evaluate side-chains 152 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.0010 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7028 Z= 0.226 Angle : 0.538 10.337 9546 Z= 0.270 Chirality : 0.042 0.198 1127 Planarity : 0.003 0.048 1188 Dihedral : 5.573 72.677 995 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.35 % Allowed : 14.66 % Favored : 81.98 % 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 (0.28), residues: 880 helix: 2.12 (0.27), residues: 368 sheet: 0.37 (0.38), residues: 182 loop : -1.12 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.002 PHE R 205 TYR 0.011 0.001 TYR R 98 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8581 (m-40) cc_final: 0.8336 (m-40) REVERT: A 24 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7019 (ttm110) REVERT: R 27 ARG cc_start: 0.7289 (ttm110) cc_final: 0.6968 (ttm-80) REVERT: R 174 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7424 (tt) REVERT: R 229 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.6882 (ttt90) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 1.1289 time to fit residues: 174.2158 Evaluate side-chains 153 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0970 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7028 Z= 0.213 Angle : 0.542 11.337 9546 Z= 0.272 Chirality : 0.042 0.270 1127 Planarity : 0.003 0.048 1188 Dihedral : 5.608 73.617 995 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.07 % Allowed : 15.08 % Favored : 81.84 % 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: 0.85 (0.28), residues: 880 helix: 2.09 (0.27), residues: 368 sheet: 0.30 (0.38), residues: 184 loop : -1.06 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.002 PHE R 205 TYR 0.015 0.001 TYR R 81 ARG 0.004 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8183 (mmtp) REVERT: B 239 ASN cc_start: 0.8578 (m-40) cc_final: 0.8335 (m-40) REVERT: A 24 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7021 (ttm110) REVERT: R 27 ARG cc_start: 0.7284 (ttm110) cc_final: 0.6962 (ttm-80) REVERT: R 92 LEU cc_start: 0.8949 (tp) cc_final: 0.8729 (tm) REVERT: R 174 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7383 (tt) REVERT: R 229 ARG cc_start: 0.7517 (ttp-170) cc_final: 0.6896 (ttt90) outliers start: 22 outliers final: 18 residues processed: 147 average time/residue: 1.1319 time to fit residues: 175.6695 Evaluate side-chains 151 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114356 restraints weight = 9755.207| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.21 r_work: 0.3053 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7028 Z= 0.221 Angle : 0.542 11.770 9546 Z= 0.271 Chirality : 0.042 0.228 1127 Planarity : 0.003 0.048 1188 Dihedral : 5.628 74.443 995 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.35 % Allowed : 14.66 % Favored : 81.98 % 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 (0.28), residues: 880 helix: 2.10 (0.27), residues: 368 sheet: 0.31 (0.38), residues: 184 loop : -1.05 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.002 PHE R 205 TYR 0.014 0.001 TYR R 81 ARG 0.004 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.76 seconds wall clock time: 60 minutes 10.88 seconds (3610.88 seconds total)