Starting phenix.real_space_refine on Wed Feb 14 15:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1v_23119/02_2024/7l1v_23119_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1v_23119/02_2024/7l1v_23119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1v_23119/02_2024/7l1v_23119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1v_23119/02_2024/7l1v_23119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1v_23119/02_2024/7l1v_23119_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1v_23119/02_2024/7l1v_23119_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6145 2.51 5 N 1649 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 374": "OE1" <-> "OE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 55": "OD1" <-> "OD2" Residue "S TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9606 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1802 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2549 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 429 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1724 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2251 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "S" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 806 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'XGD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.59 Number of scatterers: 9606 At special positions: 0 Unit cell: (107.52, 107.52, 152.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1743 8.00 N 1649 7.00 C 6145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 95 " 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: 3.21 Conformation dependent library (CDL) restraints added in 1.9 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 16 sheets defined 29.3% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 4.247A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.829A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 349 removed outlier: 4.128A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.119A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 23 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'R' and resid 56 through 81 removed outlier: 3.720A pdb=" N VAL R 66 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 106 Processing helix chain 'R' and resid 108 through 117 Processing helix chain 'R' and resid 123 through 154 Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 166 through 183 Processing helix chain 'R' and resid 185 through 189 removed outlier: 3.849A pdb=" N ILE R 189 " --> pdb=" O PRO R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 231 Processing helix chain 'R' and resid 233 through 249 Processing helix chain 'R' and resid 293 through 316 removed outlier: 4.048A pdb=" N LYS R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 328 Processing helix chain 'R' and resid 342 through 364 removed outlier: 3.709A pdb=" N TRP R 351 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU R 352 " --> pdb=" O PHE R 348 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL R 353 " --> pdb=" O SER R 349 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 375 Processing helix chain 'S' and resid 87 through 89 No H-bonds generated for 'chain 'S' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.180A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN A 218 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.932A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.904A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.694A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.996A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A 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: 6.618A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.572A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.254A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.878A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.576A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 226 through 231 removed outlier: 6.434A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 191 through 196 removed outlier: 3.684A pdb=" N PHE R 207 " --> pdb=" O VAL R 196 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= P, first strand: chain 'S' and resid 108 through 110 removed outlier: 6.291A pdb=" N ARG S 37 " --> pdb=" O TRP S 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TRP S 46 " --> pdb=" O ARG S 37 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA S 39 " --> pdb=" O ARG S 44 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG S 44 " --> pdb=" O ALA S 39 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1194 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: 2.59 Time building geometry restraints manager: 3.57 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: 2883 1.34 - 1.46: 2221 1.46 - 1.58: 4616 1.58 - 1.70: 1 1.70 - 1.82: 101 Bond restraints: 9822 Sorted by residual: bond pdb=" C LEU R 108 " pdb=" N PRO R 109 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.87e+01 bond pdb=" CG LEU A 46 " pdb=" CD1 LEU A 46 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 bond pdb=" N XGD R 401 " pdb=" S XGD R 401 " ideal model delta sigma weight residual 1.672 1.631 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CA THR R 204 " pdb=" C THR R 204 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.51e-02 4.39e+03 3.01e+00 bond pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.87e+00 ... (remaining 9817 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.86: 173 105.86 - 112.91: 5177 112.91 - 119.97: 3472 119.97 - 127.02: 4417 127.02 - 134.08: 121 Bond angle restraints: 13360 Sorted by residual: angle pdb=" C XGD R 401 " pdb=" N XGD R 401 " pdb=" S XGD R 401 " ideal model delta sigma weight residual 116.72 132.21 -15.49 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C GLN H 183 " pdb=" N SER H 184 " pdb=" CA SER H 184 " ideal model delta sigma weight residual 120.97 131.35 -10.38 2.84e+00 1.24e-01 1.34e+01 angle pdb=" CA LEU B 146 " pdb=" CB LEU B 146 " pdb=" CG LEU B 146 " ideal model delta sigma weight residual 116.30 128.78 -12.48 3.50e+00 8.16e-02 1.27e+01 angle pdb=" C CYS R 107 " pdb=" N LEU R 108 " pdb=" CA LEU R 108 " ideal model delta sigma weight residual 120.26 124.91 -4.65 1.34e+00 5.57e-01 1.20e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5285 17.81 - 35.62: 394 35.62 - 53.43: 62 53.43 - 71.24: 11 71.24 - 89.05: 1 Dihedral angle restraints: 5753 sinusoidal: 2114 harmonic: 3639 Sorted by residual: dihedral pdb=" CA PHE R 121 " pdb=" C PHE R 121 " pdb=" N PHE R 122 " pdb=" CA PHE R 122 " ideal model delta harmonic sigma weight residual 180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.16 45.84 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 934 0.044 - 0.088: 432 0.088 - 0.132: 122 0.132 - 0.176: 33 0.176 - 0.220: 8 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB THR H 116 " pdb=" CA THR H 116 " pdb=" OG1 THR H 116 " pdb=" CG2 THR H 116 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL S 97 " pdb=" CA VAL S 97 " pdb=" CG1 VAL S 97 " pdb=" CG2 VAL S 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL B 200 " pdb=" CA VAL B 200 " pdb=" CG1 VAL B 200 " pdb=" CG2 VAL B 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 1526 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N XGD R 401 " -0.178 2.00e-02 2.50e+03 1.19e-01 2.85e+02 pdb=" C XGD R 401 " 0.114 2.00e-02 2.50e+03 pdb=" C1 XGD R 401 " 0.196 2.00e-02 2.50e+03 pdb=" C14 XGD R 401 " -0.013 2.00e-02 2.50e+03 pdb=" C15 XGD R 401 " -0.051 2.00e-02 2.50e+03 pdb=" C16 XGD R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C2 XGD R 401 " 0.080 2.00e-02 2.50e+03 pdb=" C3 XGD R 401 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O XGD R 401 " 0.018 2.00e-02 2.50e+03 9.42e-02 1.11e+02 pdb=" C4 XGD R 401 " -0.115 2.00e-02 2.50e+03 pdb=" C5 XGD R 401 " 0.043 2.00e-02 2.50e+03 pdb=" C6 XGD R 401 " -0.090 2.00e-02 2.50e+03 pdb=" N1 XGD R 401 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 XGD R 401 " 0.071 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" C20 XGD R 401 " -0.043 2.00e-02 2.50e+03 pdb=" C21 XGD R 401 " -0.017 2.00e-02 2.50e+03 pdb=" C22 XGD R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C23 XGD R 401 " 0.020 2.00e-02 2.50e+03 pdb=" C24 XGD R 401 " -0.026 2.00e-02 2.50e+03 pdb=" C25 XGD R 401 " 0.045 2.00e-02 2.50e+03 pdb=" C28 XGD R 401 " -0.067 2.00e-02 2.50e+03 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3009 2.82 - 3.34: 7908 3.34 - 3.86: 15716 3.86 - 4.38: 18175 4.38 - 4.90: 32919 Nonbonded interactions: 77727 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.306 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.315 2.440 nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR H 175 " model vdw 2.322 2.440 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.341 2.520 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.343 2.440 ... (remaining 77722 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: 1.420 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: 0.000 Extract box with map and model: 6.020 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.140 Find NCS groups from input model: 0.240 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.007 0.071 9822 Z= 0.479 Angle : 0.912 15.494 13360 Z= 0.508 Chirality : 0.056 0.220 1529 Planarity : 0.008 0.119 1681 Dihedral : 12.816 89.055 3397 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.30 % Allowed : 6.36 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1235 helix: -1.94 (0.20), residues: 383 sheet: -1.12 (0.26), residues: 341 loop : -2.37 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS H 35 PHE 0.021 0.003 PHE B 241 TYR 0.028 0.003 TYR B 59 ARG 0.005 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.136 Fit side-chains REVERT: H 3 GLN cc_start: 0.7596 (pt0) cc_final: 0.7291 (pt0) REVERT: H 69 THR cc_start: 0.7814 (t) cc_final: 0.7593 (m) REVERT: H 202 ARG cc_start: 0.8570 (ptt-90) cc_final: 0.8086 (ptt180) REVERT: R 151 ASP cc_start: 0.8165 (t70) cc_final: 0.7810 (t0) REVERT: R 213 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7393 (ttt180) REVERT: R 249 LYS cc_start: 0.7883 (tptm) cc_final: 0.7488 (tppt) REVERT: R 327 LYS cc_start: 0.8509 (tttt) cc_final: 0.8300 (tttm) REVERT: S 32 VAL cc_start: 0.8544 (t) cc_final: 0.8321 (p) outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 1.4681 time to fit residues: 262.9969 Evaluate side-chains 118 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 385 GLN B 62 HIS B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN H 13 GLN H 142 GLN H 171 ASN H 183 GLN R 83 HIS S 38 GLN S 104 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9822 Z= 0.185 Angle : 0.522 5.966 13360 Z= 0.278 Chirality : 0.042 0.138 1529 Planarity : 0.004 0.041 1681 Dihedral : 5.662 50.223 1381 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.92 % Allowed : 14.04 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1235 helix: 0.02 (0.25), residues: 390 sheet: -0.56 (0.27), residues: 327 loop : -1.92 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS R 224 PHE 0.012 0.001 PHE R 122 TYR 0.013 0.001 TYR S 103 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.165 Fit side-chains REVERT: H 3 GLN cc_start: 0.7656 (pt0) cc_final: 0.7369 (pt0) REVERT: R 151 ASP cc_start: 0.8158 (t70) cc_final: 0.7812 (t0) REVERT: R 249 LYS cc_start: 0.7802 (tptm) cc_final: 0.7481 (tppt) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 1.3241 time to fit residues: 203.8249 Evaluate side-chains 127 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 0.0010 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 392 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9822 Z= 0.291 Angle : 0.557 7.225 13360 Z= 0.296 Chirality : 0.044 0.188 1529 Planarity : 0.004 0.042 1681 Dihedral : 5.600 49.304 1381 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.13 % Allowed : 15.35 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1235 helix: 0.80 (0.26), residues: 386 sheet: -0.43 (0.28), residues: 315 loop : -1.70 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.002 PHE R 227 TYR 0.014 0.002 TYR A 339 ARG 0.010 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.104 Fit side-chains REVERT: B 59 TYR cc_start: 0.8336 (m-80) cc_final: 0.7522 (m-80) REVERT: B 75 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8280 (tp40) REVERT: H 3 GLN cc_start: 0.7708 (pt0) cc_final: 0.7428 (pt0) REVERT: R 151 ASP cc_start: 0.8109 (t70) cc_final: 0.7747 (t0) REVERT: R 249 LYS cc_start: 0.7911 (tptm) cc_final: 0.7578 (tppt) outliers start: 31 outliers final: 20 residues processed: 138 average time/residue: 1.2768 time to fit residues: 188.7289 Evaluate side-chains 134 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 251 TRP Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9822 Z= 0.311 Angle : 0.561 7.386 13360 Z= 0.297 Chirality : 0.044 0.178 1529 Planarity : 0.004 0.045 1681 Dihedral : 5.564 48.135 1381 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.04 % Allowed : 15.56 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1235 helix: 1.16 (0.26), residues: 386 sheet: -0.29 (0.28), residues: 308 loop : -1.56 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.002 PHE R 227 TYR 0.018 0.002 TYR S 103 ARG 0.010 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.325 Fit side-chains REVERT: B 59 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: B 75 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8280 (tp40) REVERT: B 234 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: H 3 GLN cc_start: 0.7738 (pt0) cc_final: 0.7460 (pt0) REVERT: R 151 ASP cc_start: 0.8110 (t70) cc_final: 0.7789 (t0) REVERT: R 249 LYS cc_start: 0.7909 (tptm) cc_final: 0.7571 (tppt) REVERT: R 297 ARG cc_start: 0.7320 (ttt-90) cc_final: 0.6982 (mmt180) REVERT: S 81 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: S 103 TYR cc_start: 0.8173 (t80) cc_final: 0.7929 (t80) outliers start: 40 outliers final: 27 residues processed: 143 average time/residue: 1.2927 time to fit residues: 197.9608 Evaluate side-chains 146 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 251 TRP Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9822 Z= 0.231 Angle : 0.519 6.112 13360 Z= 0.274 Chirality : 0.042 0.168 1529 Planarity : 0.004 0.046 1681 Dihedral : 5.261 45.210 1381 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.64 % Allowed : 17.07 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.23), residues: 1235 helix: 1.46 (0.26), residues: 386 sheet: -0.22 (0.28), residues: 315 loop : -1.33 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.012 0.002 PHE R 227 TYR 0.013 0.001 TYR A 339 ARG 0.010 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.165 Fit side-chains REVERT: A 221 MET cc_start: 0.8622 (ttm) cc_final: 0.8218 (ttp) REVERT: B 59 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: B 75 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8184 (tp40) REVERT: B 234 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8755 (m-80) REVERT: H 3 GLN cc_start: 0.7716 (pt0) cc_final: 0.7449 (pt0) REVERT: R 151 ASP cc_start: 0.8084 (t70) cc_final: 0.7791 (t0) REVERT: R 249 LYS cc_start: 0.7895 (tptm) cc_final: 0.7542 (tppt) outliers start: 36 outliers final: 24 residues processed: 151 average time/residue: 1.1959 time to fit residues: 194.0420 Evaluate side-chains 147 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 392 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS S 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9822 Z= 0.292 Angle : 0.547 6.868 13360 Z= 0.289 Chirality : 0.044 0.162 1529 Planarity : 0.004 0.051 1681 Dihedral : 5.390 45.384 1381 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.43 % Allowed : 17.98 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.23), residues: 1235 helix: 1.53 (0.26), residues: 386 sheet: -0.24 (0.27), residues: 318 loop : -1.22 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.013 0.002 PHE R 227 TYR 0.014 0.001 TYR A 339 ARG 0.012 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.183 Fit side-chains REVERT: A 221 MET cc_start: 0.8599 (ttm) cc_final: 0.8203 (ttp) REVERT: B 59 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: C 58 GLU cc_start: 0.8059 (mp0) cc_final: 0.7553 (pm20) REVERT: H 3 GLN cc_start: 0.7746 (pt0) cc_final: 0.7477 (pt0) REVERT: R 151 ASP cc_start: 0.8085 (t70) cc_final: 0.7809 (t0) REVERT: R 249 LYS cc_start: 0.7897 (tptm) cc_final: 0.7538 (tppt) REVERT: R 297 ARG cc_start: 0.7331 (ttt-90) cc_final: 0.6947 (mmt180) outliers start: 34 outliers final: 26 residues processed: 142 average time/residue: 1.3153 time to fit residues: 199.9667 Evaluate side-chains 146 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9822 Z= 0.173 Angle : 0.492 8.555 13360 Z= 0.259 Chirality : 0.041 0.158 1529 Planarity : 0.003 0.053 1681 Dihedral : 4.954 42.926 1381 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.03 % Allowed : 19.19 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.24), residues: 1235 helix: 1.76 (0.26), residues: 386 sheet: -0.07 (0.28), residues: 327 loop : -1.05 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.011 0.001 PHE R 227 TYR 0.020 0.001 TYR S 103 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.147 Fit side-chains REVERT: B 59 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8731 (m-80) REVERT: B 293 ASN cc_start: 0.8200 (p0) cc_final: 0.7895 (p0) REVERT: C 58 GLU cc_start: 0.8083 (mp0) cc_final: 0.7621 (pm20) REVERT: H 3 GLN cc_start: 0.7710 (pt0) cc_final: 0.7472 (pt0) REVERT: R 151 ASP cc_start: 0.8066 (t70) cc_final: 0.7821 (t0) REVERT: R 249 LYS cc_start: 0.7884 (tptm) cc_final: 0.7513 (tppt) REVERT: S 82 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6632 (mpp) outliers start: 30 outliers final: 20 residues processed: 138 average time/residue: 1.1856 time to fit residues: 176.0542 Evaluate side-chains 138 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9822 Z= 0.335 Angle : 0.569 8.771 13360 Z= 0.298 Chirality : 0.044 0.156 1529 Planarity : 0.004 0.060 1681 Dihedral : 5.343 45.112 1381 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.03 % Allowed : 19.29 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.24), residues: 1235 helix: 1.64 (0.26), residues: 386 sheet: -0.24 (0.28), residues: 324 loop : -1.03 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.014 0.002 PHE R 227 TYR 0.014 0.002 TYR A 339 ARG 0.013 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.079 Fit side-chains REVERT: A 221 MET cc_start: 0.8611 (ttm) cc_final: 0.8234 (ttp) REVERT: B 59 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 234 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8778 (m-80) REVERT: C 58 GLU cc_start: 0.8094 (mp0) cc_final: 0.7626 (pm20) REVERT: H 3 GLN cc_start: 0.7757 (pt0) cc_final: 0.7491 (pt0) REVERT: R 151 ASP cc_start: 0.8122 (t70) cc_final: 0.7823 (t0) REVERT: R 249 LYS cc_start: 0.7915 (tptm) cc_final: 0.7562 (tppt) REVERT: R 297 ARG cc_start: 0.7342 (ttt-90) cc_final: 0.7004 (mpt180) REVERT: S 82 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6597 (mpp) outliers start: 30 outliers final: 23 residues processed: 135 average time/residue: 1.2637 time to fit residues: 182.6996 Evaluate side-chains 140 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9822 Z= 0.263 Angle : 0.537 8.453 13360 Z= 0.282 Chirality : 0.043 0.154 1529 Planarity : 0.004 0.062 1681 Dihedral : 5.194 42.698 1381 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.13 % Allowed : 19.39 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.24), residues: 1235 helix: 1.72 (0.26), residues: 386 sheet: -0.22 (0.27), residues: 339 loop : -0.95 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.013 0.002 PHE R 227 TYR 0.013 0.001 TYR A 339 ARG 0.014 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.156 Fit side-chains REVERT: A 221 MET cc_start: 0.8621 (ttm) cc_final: 0.8226 (ttp) REVERT: B 59 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 197 ARG cc_start: 0.7680 (ptp-110) cc_final: 0.7346 (ptt90) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: C 58 GLU cc_start: 0.8104 (mp0) cc_final: 0.7673 (pm20) REVERT: H 3 GLN cc_start: 0.7735 (pt0) cc_final: 0.7471 (pt0) REVERT: R 151 ASP cc_start: 0.8109 (t70) cc_final: 0.7835 (t0) REVERT: R 249 LYS cc_start: 0.7896 (tptm) cc_final: 0.7544 (tppt) REVERT: R 297 ARG cc_start: 0.7351 (ttt-90) cc_final: 0.7003 (mpt180) REVERT: S 82 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6629 (mpp) outliers start: 31 outliers final: 24 residues processed: 134 average time/residue: 1.2163 time to fit residues: 175.1899 Evaluate side-chains 138 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9822 Z= 0.185 Angle : 0.502 8.213 13360 Z= 0.264 Chirality : 0.042 0.153 1529 Planarity : 0.004 0.059 1681 Dihedral : 4.895 38.064 1381 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.93 % Allowed : 19.80 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.28 (0.24), residues: 1235 helix: 1.87 (0.26), residues: 386 sheet: -0.15 (0.27), residues: 341 loop : -0.85 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.017 0.001 PHE R 122 TYR 0.011 0.001 TYR A 339 ARG 0.014 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.155 Fit side-chains REVERT: A 221 MET cc_start: 0.8612 (ttm) cc_final: 0.8232 (ttp) REVERT: B 59 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: B 197 ARG cc_start: 0.7588 (ptp-110) cc_final: 0.7234 (ptt90) REVERT: B 234 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: C 58 GLU cc_start: 0.8125 (mp0) cc_final: 0.7686 (pm20) REVERT: H 3 GLN cc_start: 0.7703 (pt0) cc_final: 0.7461 (pt0) REVERT: R 151 ASP cc_start: 0.8053 (t70) cc_final: 0.7820 (t0) REVERT: R 249 LYS cc_start: 0.7903 (tptm) cc_final: 0.7529 (tppt) REVERT: S 82 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6628 (mpp) outliers start: 29 outliers final: 22 residues processed: 132 average time/residue: 1.1127 time to fit residues: 158.3630 Evaluate side-chains 136 residues out of total 1073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117354 restraints weight = 12435.921| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.92 r_work: 0.3359 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9822 Z= 0.238 Angle : 0.528 8.169 13360 Z= 0.277 Chirality : 0.043 0.153 1529 Planarity : 0.004 0.058 1681 Dihedral : 4.953 38.116 1381 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.73 % Allowed : 20.20 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.27 (0.24), residues: 1235 helix: 1.87 (0.26), residues: 386 sheet: -0.21 (0.27), residues: 346 loop : -0.83 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS B 142 PHE 0.017 0.002 PHE R 122 TYR 0.012 0.001 TYR A 339 ARG 0.013 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3684.32 seconds wall clock time: 66 minutes 20.90 seconds (3980.90 seconds total)