Starting phenix.real_space_refine on Sat Apr 6 10:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxv_36714/04_2024/8jxv_36714_updated.pdb" } resolution = 3.21 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= 0.016 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 Cl 1 4.86 5 C 5111 2.51 5 N 1307 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 155": "OE1" <-> "OE2" Residue "R PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7935 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1550 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 201} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2293 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 300} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 227 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 27} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1749 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2093 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'VBU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.48, per 1000 atoms: 0.56 Number of scatterers: 7935 At special positions: 0 Unit cell: (83.6, 118.8, 129.8, 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 52 16.00 O 1464 8.00 N 1307 7.00 C 5111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 30.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.763A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.193A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 347 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 16 through 42 removed outlier: 4.002A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 62 Processing helix chain 'R' and resid 68 through 77 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 84 through 117 removed outlier: 4.748A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 150 removed outlier: 4.324A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 184 through 202 Processing helix chain 'R' and resid 294 through 328 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 338 through 361 removed outlier: 3.788A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 4.129A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 363 through 371 Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 7.402A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.762A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.939A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 148 through 153 removed outlier: 3.753A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 160 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.681A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.279A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.250A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.855A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.708A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.888A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 156 through 161 345 hydrogen bonds defined for protein. 978 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: 2.17 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2491 1.34 - 1.46: 2032 1.46 - 1.58: 3522 1.58 - 1.70: 2 1.70 - 1.82: 74 Bond restraints: 8121 Sorted by residual: bond pdb=" C10 VBU R 401 " pdb=" N02 VBU R 401 " ideal model delta sigma weight residual 1.448 1.618 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C10 VBU R 401 " pdb=" N04 VBU R 401 " ideal model delta sigma weight residual 1.447 1.303 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C10 VBU R 401 " pdb=" C11 VBU R 401 " ideal model delta sigma weight residual 1.543 1.624 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C07 VBU R 401 " pdb=" N02 VBU R 401 " ideal model delta sigma weight residual 1.470 1.543 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C06 VBU R 401 " pdb=" N02 VBU R 401 " ideal model delta sigma weight residual 1.468 1.534 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 8116 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.52: 173 106.52 - 113.80: 4554 113.80 - 121.08: 3955 121.08 - 128.36: 2296 128.36 - 135.64: 76 Bond angle restraints: 11054 Sorted by residual: angle pdb=" C21 VBU R 401 " pdb=" C15 VBU R 401 " pdb=" N05 VBU R 401 " ideal model delta sigma weight residual 109.84 125.56 -15.72 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C10 VBU R 401 " pdb=" N04 VBU R 401 " pdb=" C14 VBU R 401 " ideal model delta sigma weight residual 120.04 135.64 -15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C13 VBU R 401 " pdb=" N05 VBU R 401 " pdb=" C15 VBU R 401 " ideal model delta sigma weight residual 111.03 124.09 -13.06 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C08 VBU R 401 " pdb=" N03 VBU R 401 " pdb=" C09 VBU R 401 " ideal model delta sigma weight residual 112.38 100.44 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C10 VBU R 401 " pdb=" C11 VBU R 401 " pdb=" C16 VBU R 401 " ideal model delta sigma weight residual 120.02 130.56 -10.54 3.00e+00 1.11e-01 1.24e+01 ... (remaining 11049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4272 16.79 - 33.57: 340 33.57 - 50.36: 73 50.36 - 67.15: 8 67.15 - 83.93: 5 Dihedral angle restraints: 4698 sinusoidal: 1682 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.04 -45.04 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA PHE E 80 " pdb=" C PHE E 80 " pdb=" N LEU E 81 " pdb=" CA LEU E 81 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG E 192 " pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 805 0.038 - 0.076: 332 0.076 - 0.114: 110 0.114 - 0.153: 24 0.153 - 0.191: 4 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA PRO R 186 " pdb=" N PRO R 186 " pdb=" C PRO R 186 " pdb=" CB PRO R 186 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA TRP R 316 " pdb=" N TRP R 316 " pdb=" C TRP R 316 " pdb=" CB TRP R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA TYR C 59 " pdb=" N TYR C 59 " pdb=" C TYR C 59 " pdb=" CB TYR C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 1272 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 306 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C GLY C 306 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY C 306 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL C 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " -0.019 2.00e-02 2.50e+03 1.64e-02 6.73e+00 pdb=" CG TRP C 332 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.041 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO R 355 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.034 5.00e-02 4.00e+02 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 94 2.63 - 3.20: 7213 3.20 - 3.77: 11953 3.77 - 4.33: 16125 4.33 - 4.90: 27269 Nonbonded interactions: 62654 Sorted by model distance: nonbonded pdb=" OG SER C 275 " pdb=" O SER C 316 " model vdw 2.068 2.440 nonbonded pdb=" O ARG E 67 " pdb=" OG1 THR E 84 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.220 2.440 nonbonded pdb=" O CYS C 103 " pdb=" NH1 ARG C 150 " model vdw 2.227 2.520 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.241 2.440 ... (remaining 62649 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.910 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.880 Find NCS groups from input model: 0.260 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.170 8121 Z= 0.414 Angle : 0.845 15.721 11054 Z= 0.435 Chirality : 0.046 0.191 1275 Planarity : 0.004 0.061 1379 Dihedral : 13.191 83.932 2744 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1016 helix: 1.11 (0.30), residues: 302 sheet: -0.28 (0.33), residues: 243 loop : -1.71 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 332 HIS 0.004 0.001 HIS B 322 PHE 0.021 0.002 PHE C 234 TYR 0.012 0.002 TYR E 95 ARG 0.006 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.841 Fit side-chains REVERT: C 332 TRP cc_start: 0.6650 (m-10) cc_final: 0.6368 (m-10) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1921 time to fit residues: 30.8959 Evaluate side-chains 106 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8121 Z= 0.197 Angle : 0.650 11.789 11054 Z= 0.326 Chirality : 0.042 0.150 1275 Planarity : 0.004 0.049 1379 Dihedral : 6.297 74.694 1115 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.85 % Allowed : 7.51 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1016 helix: 1.52 (0.30), residues: 301 sheet: -0.28 (0.31), residues: 283 loop : -1.59 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.002 0.001 HIS C 311 PHE 0.014 0.002 PHE C 253 TYR 0.010 0.001 TYR R 329 ARG 0.002 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.989 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 113 average time/residue: 0.2005 time to fit residues: 31.1238 Evaluate side-chains 106 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 143 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8121 Z= 0.166 Angle : 0.604 10.956 11054 Z= 0.303 Chirality : 0.041 0.142 1275 Planarity : 0.004 0.044 1379 Dihedral : 6.017 72.599 1115 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.45 % Allowed : 9.20 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1016 helix: 1.77 (0.30), residues: 301 sheet: -0.17 (0.31), residues: 289 loop : -1.52 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.002 0.001 HIS C 142 PHE 0.013 0.001 PHE C 253 TYR 0.008 0.001 TYR R 329 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: E 177 TRP cc_start: 0.6026 (m100) cc_final: 0.5550 (m100) REVERT: R 150 MET cc_start: 0.8187 (tpp) cc_final: 0.7576 (mmt) REVERT: R 322 PHE cc_start: 0.7059 (t80) cc_final: 0.6797 (t80) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.1947 time to fit residues: 30.8071 Evaluate side-chains 111 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 44 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8121 Z= 0.142 Angle : 0.584 9.885 11054 Z= 0.290 Chirality : 0.040 0.146 1275 Planarity : 0.004 0.044 1379 Dihedral : 5.893 72.559 1115 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.82 % Allowed : 11.50 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 1016 helix: 1.97 (0.31), residues: 301 sheet: -0.02 (0.32), residues: 284 loop : -1.39 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.002 0.000 HIS C 142 PHE 0.026 0.002 PHE E 29 TYR 0.010 0.001 TYR R 319 ARG 0.002 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 322 PHE cc_start: 0.7172 (t80) cc_final: 0.6958 (t80) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.2026 time to fit residues: 33.7861 Evaluate side-chains 112 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8121 Z= 0.188 Angle : 0.610 10.038 11054 Z= 0.302 Chirality : 0.041 0.136 1275 Planarity : 0.004 0.045 1379 Dihedral : 5.833 75.096 1115 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.18 % Allowed : 13.20 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1016 helix: 2.02 (0.31), residues: 302 sheet: 0.06 (0.32), residues: 278 loop : -1.37 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 47 HIS 0.002 0.001 HIS C 311 PHE 0.021 0.002 PHE E 29 TYR 0.009 0.001 TYR E 102 ARG 0.005 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.897 Fit side-chains REVERT: B 266 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5887 (tt) REVERT: E 177 TRP cc_start: 0.5784 (m100) cc_final: 0.5264 (m100) REVERT: R 322 PHE cc_start: 0.7215 (t80) cc_final: 0.7006 (t80) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.1873 time to fit residues: 31.0282 Evaluate side-chains 118 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8121 Z= 0.204 Angle : 0.617 10.219 11054 Z= 0.305 Chirality : 0.041 0.142 1275 Planarity : 0.004 0.045 1379 Dihedral : 5.819 73.888 1115 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.27 % Allowed : 12.95 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1016 helix: 1.97 (0.31), residues: 302 sheet: 0.04 (0.32), residues: 278 loop : -1.32 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.002 0.001 HIS C 142 PHE 0.014 0.002 PHE C 180 TYR 0.009 0.001 TYR E 102 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.825 Fit side-chains REVERT: B 4 THR cc_start: 0.6842 (OUTLIER) cc_final: 0.6539 (m) REVERT: B 266 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5781 (tt) outliers start: 27 outliers final: 17 residues processed: 124 average time/residue: 0.1784 time to fit residues: 31.3028 Evaluate side-chains 123 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8121 Z= 0.228 Angle : 0.638 10.596 11054 Z= 0.316 Chirality : 0.041 0.145 1275 Planarity : 0.004 0.047 1379 Dihedral : 5.825 72.548 1115 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.91 % Allowed : 13.92 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1016 helix: 1.89 (0.30), residues: 302 sheet: 0.05 (0.32), residues: 282 loop : -1.28 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.002 PHE B 250 TYR 0.010 0.001 TYR E 102 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.913 Fit side-chains REVERT: B 4 THR cc_start: 0.6842 (OUTLIER) cc_final: 0.6538 (m) REVERT: B 266 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6050 (tt) REVERT: E 177 TRP cc_start: 0.5809 (m100) cc_final: 0.5361 (m100) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.1901 time to fit residues: 32.0216 Evaluate side-chains 126 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8121 Z= 0.138 Angle : 0.584 9.716 11054 Z= 0.287 Chirality : 0.040 0.155 1275 Planarity : 0.004 0.044 1379 Dihedral : 5.632 70.541 1115 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.82 % Allowed : 15.50 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1016 helix: 2.10 (0.31), residues: 302 sheet: 0.16 (0.32), residues: 279 loop : -1.15 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.001 0.000 HIS C 142 PHE 0.016 0.001 PHE E 29 TYR 0.007 0.001 TYR R 72 ARG 0.002 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.691 Fit side-chains REVERT: B 4 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6511 (m) REVERT: E 193 MET cc_start: 0.6262 (ttp) cc_final: 0.6062 (tmm) REVERT: R 150 MET cc_start: 0.8015 (tpp) cc_final: 0.7772 (mmm) outliers start: 15 outliers final: 13 residues processed: 113 average time/residue: 0.1876 time to fit residues: 29.7673 Evaluate side-chains 115 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8121 Z= 0.269 Angle : 0.660 10.475 11054 Z= 0.328 Chirality : 0.042 0.154 1275 Planarity : 0.004 0.045 1379 Dihedral : 5.798 71.812 1115 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.66 % Allowed : 15.25 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1016 helix: 1.86 (0.30), residues: 303 sheet: 0.04 (0.31), residues: 282 loop : -1.19 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 332 HIS 0.003 0.001 HIS B 322 PHE 0.019 0.002 PHE C 180 TYR 0.020 0.002 TYR R 319 ARG 0.006 0.000 ARG R 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 0.906 Fit side-chains REVERT: B 4 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6485 (m) REVERT: E 177 TRP cc_start: 0.5938 (m100) cc_final: 0.5511 (m100) REVERT: R 150 MET cc_start: 0.8142 (tpp) cc_final: 0.7449 (mmt) outliers start: 22 outliers final: 18 residues processed: 120 average time/residue: 0.1917 time to fit residues: 32.2462 Evaluate side-chains 123 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 307 ILE Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.6980 chunk 93 optimal weight: 0.0270 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 74 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8121 Z= 0.155 Angle : 0.604 9.794 11054 Z= 0.297 Chirality : 0.040 0.143 1275 Planarity : 0.004 0.043 1379 Dihedral : 5.640 70.908 1115 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.94 % Allowed : 15.86 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1016 helix: 2.05 (0.30), residues: 302 sheet: 0.12 (0.32), residues: 273 loop : -1.16 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 345 HIS 0.002 0.001 HIS E 35 PHE 0.015 0.001 PHE E 29 TYR 0.017 0.001 TYR R 192 ARG 0.004 0.000 ARG R 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.897 Fit side-chains REVERT: B 4 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6517 (m) REVERT: E 177 TRP cc_start: 0.5737 (m100) cc_final: 0.5284 (m100) REVERT: R 150 MET cc_start: 0.8047 (tpp) cc_final: 0.7468 (mmt) outliers start: 16 outliers final: 14 residues processed: 119 average time/residue: 0.1858 time to fit residues: 30.6829 Evaluate side-chains 120 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 232 GLN ** 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 = 0.4262 r_free = 0.4262 target = 0.146050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.122981 restraints weight = 13266.215| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.23 r_work: 0.3789 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8121 Z= 0.293 Angle : 0.679 10.996 11054 Z= 0.338 Chirality : 0.043 0.158 1275 Planarity : 0.004 0.046 1379 Dihedral : 5.839 71.845 1115 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.06 % Allowed : 15.86 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1016 helix: 1.82 (0.30), residues: 303 sheet: -0.00 (0.31), residues: 282 loop : -1.17 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 332 HIS 0.004 0.001 HIS C 311 PHE 0.020 0.002 PHE C 180 TYR 0.014 0.002 TYR R 319 ARG 0.007 0.000 ARG R 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.50 seconds wall clock time: 36 minutes 3.43 seconds (2163.43 seconds total)