Starting phenix.real_space_refine on Thu Mar 14 14:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew2_31345/03_2024/7ew2_31345_updated.pdb" } resolution = 3.1 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= 0.003 sd= 0.052 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 48 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 P 1 5.49 5 S 68 5.16 5 C 5731 2.51 5 N 1531 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ARG 217": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 307": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9001 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2320 Unusual residues: {'J89': 1} Classifications: {'peptide': 290, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 281, None: 1} Not linked: pdbres="LEU R 312 " pdbres="J89 R 401 " Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.15, per 1000 atoms: 0.57 Number of scatterers: 9001 At special positions: 0 Unit cell: (93.5, 121.55, 130.9, 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 68 16.00 P 1 15.00 O 1670 8.00 N 1531 7.00 C 5731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.04 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " 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: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 33.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 Processing helix chain 'A' and resid 46 through 52 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 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.077A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.850A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 31 through 34 No H-bonds generated for 'chain 'B' and resid 31 through 34' Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.742A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'R' and resid 17 through 25 Processing helix chain 'R' and resid 40 through 66 Processing helix chain 'R' and resid 74 through 99 Processing helix chain 'R' and resid 108 through 141 removed outlier: 3.716A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 130 " --> pdb=" O THR R 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA R 131 " --> pdb=" O CYS R 127 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 169 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 194 through 228 removed outlier: 3.788A pdb=" N ARG R 217 " --> pdb=" O ILE R 213 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 268 removed outlier: 3.711A pdb=" N CYS R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 275 through 292 removed outlier: 3.540A pdb=" N ALA R 280 " --> pdb=" O LEU R 277 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN R 281 " --> pdb=" O PHE R 278 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL R 285 " --> pdb=" O TRP R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 303 through 311 Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.874A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.757A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.679A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.520A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.687A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.873A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.848A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.931A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 155 through 160 367 hydrogen bonds defined for protein. 1026 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: 2.49 Time building geometry restraints manager: 3.67 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: 1453 1.29 - 1.42: 2419 1.42 - 1.56: 5210 1.56 - 1.69: 1 1.69 - 1.82: 99 Bond restraints: 9182 Sorted by residual: bond pdb=" CA CYS R 127 " pdb=" C CYS R 127 " ideal model delta sigma weight residual 1.522 1.421 0.101 1.31e-02 5.83e+03 5.92e+01 bond pdb=" C SER R 125 " pdb=" O SER R 125 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.17e-02 7.31e+03 4.24e+01 bond pdb=" C LEU R 122 " pdb=" O LEU R 122 " ideal model delta sigma weight residual 1.237 1.165 0.071 1.17e-02 7.31e+03 3.71e+01 bond pdb=" C CYS R 127 " pdb=" O CYS R 127 " ideal model delta sigma weight residual 1.236 1.160 0.075 1.39e-02 5.18e+03 2.95e+01 bond pdb=" CA LEU R 122 " pdb=" C LEU R 122 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.30e-02 5.92e+03 2.16e+01 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 85.68 - 95.35: 3 95.35 - 105.02: 112 105.02 - 114.69: 5574 114.69 - 124.36: 6580 124.36 - 134.03: 153 Bond angle restraints: 12422 Sorted by residual: angle pdb=" N SER R 99 " pdb=" CA SER R 99 " pdb=" C SER R 99 " ideal model delta sigma weight residual 111.28 126.61 -15.33 1.09e+00 8.42e-01 1.98e+02 angle pdb=" N GLY R 100 " pdb=" CA GLY R 100 " pdb=" C GLY R 100 " ideal model delta sigma weight residual 112.50 124.66 -12.16 1.16e+00 7.43e-01 1.10e+02 angle pdb=" C16 J89 R 401 " pdb=" C17 J89 R 401 " pdb=" N26 J89 R 401 " ideal model delta sigma weight residual 109.47 85.68 23.79 3.00e+00 1.11e-01 6.29e+01 angle pdb=" C16 J89 R 401 " pdb=" C17 J89 R 401 " pdb=" C18 J89 R 401 " ideal model delta sigma weight residual 109.47 87.00 22.47 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C16 J89 R 401 " pdb=" C17 J89 R 401 " pdb=" C20 J89 R 401 " ideal model delta sigma weight residual 109.47 90.14 19.33 3.00e+00 1.11e-01 4.15e+01 ... (remaining 12417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.85: 4957 18.85 - 37.71: 428 37.71 - 56.56: 64 56.56 - 75.41: 12 75.41 - 94.26: 6 Dihedral angle restraints: 5467 sinusoidal: 2135 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 178 " pdb=" SG CYS R 178 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual 93.00 39.19 53.81 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA CYS R 185 " pdb=" C CYS R 185 " pdb=" N SER R 186 " pdb=" CA SER R 186 " ideal model delta harmonic sigma weight residual 180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1375 0.112 - 0.223: 32 0.223 - 0.335: 1 0.335 - 0.446: 3 0.446 - 0.558: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA SER R 99 " pdb=" N SER R 99 " pdb=" C SER R 99 " pdb=" CB SER R 99 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C17 J89 R 401 " pdb=" C16 J89 R 401 " pdb=" C20 J89 R 401 " pdb=" N26 J89 R 401 " both_signs ideal model delta sigma weight residual False 2.61 3.01 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA LEU R 122 " pdb=" N LEU R 122 " pdb=" C LEU R 122 " pdb=" CB LEU R 122 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 1409 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 122 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C LEU R 122 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU R 122 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY R 123 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 97 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C LEU R 97 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU R 97 " 0.021 2.00e-02 2.50e+03 pdb=" N MET R 98 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 127 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C CYS R 127 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS R 127 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 128 " -0.014 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 652 2.74 - 3.28: 8728 3.28 - 3.82: 14424 3.82 - 4.36: 16886 4.36 - 4.90: 30005 Nonbonded interactions: 70695 Sorted by model distance: nonbonded pdb=" O LEU R 168 " pdb=" OH TYR R 196 " model vdw 2.201 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.216 2.440 nonbonded pdb=" NE2 GLN S 142 " pdb=" O ALA S 241 " model vdw 2.240 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.246 2.440 nonbonded pdb=" OG SER B 279 " pdb=" OD1 ASP C 48 " model vdw 2.270 2.440 ... (remaining 70690 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.850 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 26.640 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 9182 Z= 0.222 Angle : 0.772 23.793 12422 Z= 0.424 Chirality : 0.049 0.558 1412 Planarity : 0.004 0.039 1562 Dihedral : 14.185 94.265 3306 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.61 % Allowed : 0.20 % Favored : 99.18 % 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 (0.25), residues: 1133 helix: 1.94 (0.28), residues: 368 sheet: -0.90 (0.29), residues: 303 loop : -1.37 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.003 0.001 HIS R 152 PHE 0.017 0.001 PHE B 234 TYR 0.007 0.001 TYR S 228 ARG 0.006 0.000 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 332 TRP cc_start: 0.6646 (m-10) cc_final: 0.6437 (m-10) REVERT: S 176 TRP cc_start: 0.6749 (m100) cc_final: 0.6457 (m100) REVERT: R 126 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7476 (m) REVERT: R 143 MET cc_start: 0.6990 (mmt) cc_final: 0.6729 (mmt) REVERT: R 202 SER cc_start: 0.7355 (t) cc_final: 0.7137 (m) REVERT: R 264 LEU cc_start: 0.6897 (pp) cc_final: 0.6441 (tt) REVERT: R 265 ILE cc_start: 0.6098 (tp) cc_final: 0.5755 (pt) outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.1939 time to fit residues: 39.7718 Evaluate side-chains 114 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9182 Z= 0.155 Angle : 0.508 6.484 12422 Z= 0.262 Chirality : 0.041 0.166 1412 Planarity : 0.003 0.045 1562 Dihedral : 6.080 108.011 1261 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.13 % Allowed : 8.09 % Favored : 90.79 % 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: -0.10 (0.25), residues: 1133 helix: 2.15 (0.28), residues: 376 sheet: -0.88 (0.28), residues: 306 loop : -1.37 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS B 62 PHE 0.015 0.001 PHE S 177 TYR 0.010 0.001 TYR S 228 ARG 0.005 0.000 ARG R 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.000 Fit side-chains REVERT: A 305 CYS cc_start: 0.7043 (t) cc_final: 0.6117 (p) REVERT: R 47 LEU cc_start: 0.6197 (mm) cc_final: 0.5767 (tp) REVERT: R 264 LEU cc_start: 0.6875 (pp) cc_final: 0.6338 (tt) REVERT: R 265 ILE cc_start: 0.6000 (tp) cc_final: 0.5671 (pt) outliers start: 11 outliers final: 8 residues processed: 123 average time/residue: 0.2049 time to fit residues: 35.9745 Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 163 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 171 ASN S 231 GLN R 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9182 Z= 0.254 Angle : 0.576 7.283 12422 Z= 0.298 Chirality : 0.043 0.143 1412 Planarity : 0.004 0.037 1562 Dihedral : 6.161 82.959 1255 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.64 % Allowed : 12.18 % Favored : 86.18 % 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: -0.22 (0.25), residues: 1133 helix: 2.00 (0.28), residues: 376 sheet: -0.93 (0.28), residues: 308 loop : -1.41 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 47 HIS 0.005 0.001 HIS B 62 PHE 0.017 0.002 PHE A 189 TYR 0.016 0.002 TYR R 92 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.048 Fit side-chains REVERT: A 305 CYS cc_start: 0.7231 (t) cc_final: 0.6269 (p) REVERT: R 74 MET cc_start: 0.7452 (mmm) cc_final: 0.7232 (tpt) REVERT: R 264 LEU cc_start: 0.6870 (pp) cc_final: 0.6392 (tt) REVERT: R 265 ILE cc_start: 0.6005 (tp) cc_final: 0.5693 (pt) outliers start: 16 outliers final: 12 residues processed: 121 average time/residue: 0.1904 time to fit residues: 33.1727 Evaluate side-chains 116 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.0030 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 179 GLN S 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9182 Z= 0.145 Angle : 0.488 6.873 12422 Z= 0.252 Chirality : 0.040 0.128 1412 Planarity : 0.003 0.042 1562 Dihedral : 5.579 74.757 1255 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.05 % Allowed : 13.82 % Favored : 84.14 % 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: 0.02 (0.25), residues: 1133 helix: 2.29 (0.28), residues: 375 sheet: -0.79 (0.28), residues: 301 loop : -1.36 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 332 HIS 0.004 0.001 HIS R 21 PHE 0.014 0.001 PHE S 177 TYR 0.013 0.001 TYR R 92 ARG 0.003 0.000 ARG R 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.960 Fit side-chains REVERT: A 240 MET cc_start: 0.6391 (tpp) cc_final: 0.6174 (tpt) REVERT: A 305 CYS cc_start: 0.7151 (t) cc_final: 0.6210 (p) REVERT: R 47 LEU cc_start: 0.6162 (mm) cc_final: 0.5772 (tp) REVERT: R 215 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: R 264 LEU cc_start: 0.6862 (pp) cc_final: 0.6464 (tt) REVERT: R 265 ILE cc_start: 0.5990 (tp) cc_final: 0.5681 (pt) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.1894 time to fit residues: 32.3611 Evaluate side-chains 118 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 215 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9182 Z= 0.202 Angle : 0.528 6.805 12422 Z= 0.274 Chirality : 0.041 0.131 1412 Planarity : 0.003 0.033 1562 Dihedral : 5.561 79.036 1255 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.25 % Allowed : 15.15 % Favored : 82.60 % 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 (0.25), residues: 1133 helix: 2.25 (0.27), residues: 377 sheet: -0.81 (0.28), residues: 301 loop : -1.41 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 47 HIS 0.003 0.001 HIS R 21 PHE 0.014 0.001 PHE A 189 TYR 0.011 0.001 TYR R 24 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.014 Fit side-chains REVERT: A 305 CYS cc_start: 0.7181 (t) cc_final: 0.6265 (p) REVERT: B 338 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7760 (mp) REVERT: S 18 ARG cc_start: 0.5554 (mmm160) cc_final: 0.5258 (mtp85) REVERT: R 47 LEU cc_start: 0.6113 (mm) cc_final: 0.5699 (tp) REVERT: R 74 MET cc_start: 0.7315 (mmm) cc_final: 0.7057 (mmm) REVERT: R 215 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.6971 (m-80) REVERT: R 264 LEU cc_start: 0.6858 (pp) cc_final: 0.6502 (tt) REVERT: R 265 ILE cc_start: 0.5925 (tp) cc_final: 0.5636 (pt) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.1819 time to fit residues: 31.8029 Evaluate side-chains 123 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 239 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9182 Z= 0.141 Angle : 0.485 7.539 12422 Z= 0.249 Chirality : 0.040 0.129 1412 Planarity : 0.003 0.030 1562 Dihedral : 5.234 79.678 1255 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.46 % Allowed : 15.46 % Favored : 82.09 % 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: 0.19 (0.26), residues: 1133 helix: 2.47 (0.27), residues: 376 sheet: -0.69 (0.28), residues: 308 loop : -1.31 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.003 0.001 HIS R 21 PHE 0.014 0.001 PHE S 177 TYR 0.013 0.001 TYR R 24 ARG 0.003 0.000 ARG R 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.016 Fit side-chains REVERT: A 305 CYS cc_start: 0.7110 (t) cc_final: 0.6200 (p) REVERT: B 338 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7717 (mp) REVERT: R 47 LEU cc_start: 0.6099 (mm) cc_final: 0.5725 (tp) REVERT: R 215 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7053 (m-10) REVERT: R 264 LEU cc_start: 0.6843 (pp) cc_final: 0.6506 (tt) REVERT: R 265 ILE cc_start: 0.5852 (tp) cc_final: 0.5567 (pt) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.1872 time to fit residues: 33.4070 Evaluate side-chains 123 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 239 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 66 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9182 Z= 0.130 Angle : 0.476 6.998 12422 Z= 0.248 Chirality : 0.040 0.156 1412 Planarity : 0.003 0.028 1562 Dihedral : 5.088 82.305 1255 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 16.48 % Favored : 81.68 % 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: 0.34 (0.26), residues: 1133 helix: 2.62 (0.27), residues: 376 sheet: -0.59 (0.29), residues: 302 loop : -1.26 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 21 PHE 0.013 0.001 PHE S 177 TYR 0.014 0.001 TYR R 24 ARG 0.002 0.000 ARG R 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.104 Fit side-chains REVERT: A 305 CYS cc_start: 0.7153 (t) cc_final: 0.6217 (p) REVERT: B 338 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7702 (mp) REVERT: R 47 LEU cc_start: 0.6119 (mm) cc_final: 0.5748 (tp) REVERT: R 215 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: R 264 LEU cc_start: 0.6859 (pp) cc_final: 0.6534 (tt) REVERT: R 265 ILE cc_start: 0.5785 (tp) cc_final: 0.5512 (pt) outliers start: 18 outliers final: 15 residues processed: 116 average time/residue: 0.2100 time to fit residues: 34.2418 Evaluate side-chains 123 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 239 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 239 ASN S 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9182 Z= 0.202 Angle : 0.531 9.453 12422 Z= 0.274 Chirality : 0.042 0.179 1412 Planarity : 0.003 0.029 1562 Dihedral : 5.444 89.503 1255 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.46 % Allowed : 17.20 % Favored : 80.35 % 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: 0.24 (0.26), residues: 1133 helix: 2.47 (0.27), residues: 377 sheet: -0.70 (0.28), residues: 304 loop : -1.23 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 332 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR R 24 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.023 Fit side-chains REVERT: A 305 CYS cc_start: 0.7138 (t) cc_final: 0.6244 (p) REVERT: B 332 TRP cc_start: 0.7020 (m-10) cc_final: 0.6772 (m-10) REVERT: B 338 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7729 (mp) REVERT: R 47 LEU cc_start: 0.5979 (mm) cc_final: 0.5596 (tp) REVERT: R 215 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: R 264 LEU cc_start: 0.6863 (pp) cc_final: 0.6537 (tt) REVERT: R 265 ILE cc_start: 0.5725 (tp) cc_final: 0.5467 (pt) outliers start: 24 outliers final: 20 residues processed: 115 average time/residue: 0.1858 time to fit residues: 30.9834 Evaluate side-chains 125 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9182 Z= 0.220 Angle : 0.551 7.463 12422 Z= 0.287 Chirality : 0.042 0.171 1412 Planarity : 0.003 0.031 1562 Dihedral : 5.496 87.742 1255 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.05 % Allowed : 17.81 % Favored : 80.14 % 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: 0.15 (0.26), residues: 1133 helix: 2.34 (0.27), residues: 378 sheet: -0.72 (0.28), residues: 302 loop : -1.26 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 332 HIS 0.004 0.001 HIS S 232 PHE 0.018 0.001 PHE S 239 TYR 0.013 0.002 TYR R 24 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.994 Fit side-chains REVERT: A 305 CYS cc_start: 0.7138 (t) cc_final: 0.6247 (p) REVERT: B 338 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7749 (mp) REVERT: R 47 LEU cc_start: 0.6010 (mm) cc_final: 0.5627 (tp) REVERT: R 215 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: R 264 LEU cc_start: 0.6862 (pp) cc_final: 0.6547 (tt) REVERT: R 265 ILE cc_start: 0.5750 (tp) cc_final: 0.5489 (pt) outliers start: 20 outliers final: 18 residues processed: 117 average time/residue: 0.1908 time to fit residues: 32.2670 Evaluate side-chains 124 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 104 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9182 Z= 0.138 Angle : 0.501 7.463 12422 Z= 0.259 Chirality : 0.040 0.163 1412 Planarity : 0.003 0.028 1562 Dihedral : 5.275 86.684 1255 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.05 % Allowed : 17.91 % Favored : 80.04 % 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: 0.33 (0.26), residues: 1133 helix: 2.55 (0.27), residues: 377 sheet: -0.59 (0.28), residues: 304 loop : -1.22 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 332 HIS 0.003 0.001 HIS R 21 PHE 0.014 0.001 PHE S 177 TYR 0.013 0.001 TYR R 24 ARG 0.003 0.000 ARG S 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.840 Fit side-chains REVERT: A 305 CYS cc_start: 0.7132 (t) cc_final: 0.6199 (p) REVERT: B 332 TRP cc_start: 0.6749 (m-10) cc_final: 0.6546 (m-10) REVERT: B 338 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7705 (mp) REVERT: R 47 LEU cc_start: 0.6018 (mm) cc_final: 0.5684 (tp) REVERT: R 215 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6986 (m-10) REVERT: R 264 LEU cc_start: 0.6829 (pp) cc_final: 0.6545 (tt) REVERT: R 265 ILE cc_start: 0.5709 (tp) cc_final: 0.5456 (pt) outliers start: 20 outliers final: 16 residues processed: 115 average time/residue: 0.1995 time to fit residues: 32.3652 Evaluate side-chains 121 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 0.0050 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN R 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.202606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157747 restraints weight = 10470.640| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.53 r_work: 0.3637 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 9182 Z= 0.231 Angle : 0.900 59.197 12422 Z= 0.512 Chirality : 0.046 0.810 1412 Planarity : 0.003 0.028 1562 Dihedral : 5.281 86.674 1255 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.94 % Allowed : 18.12 % Favored : 79.94 % Cbeta Deviations : 0.09 % 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: 0.33 (0.26), residues: 1133 helix: 2.56 (0.27), residues: 377 sheet: -0.59 (0.28), residues: 304 loop : -1.23 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 332 HIS 0.003 0.001 HIS R 21 PHE 0.014 0.001 PHE S 177 TYR 0.011 0.001 TYR R 24 ARG 0.003 0.000 ARG S 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.62 seconds wall clock time: 38 minutes 56.61 seconds (2336.61 seconds total)