Starting phenix.real_space_refine on Tue Feb 13 22:26:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/02_2024/7cx2_30489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/02_2024/7cx2_30489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/02_2024/7cx2_30489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/02_2024/7cx2_30489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/02_2024/7cx2_30489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/02_2024/7cx2_30489_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 52 5.16 5 C 5027 2.51 5 N 1374 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 105": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2027 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.65, per 1000 atoms: 0.59 Number of scatterers: 7930 At special positions: 0 Unit cell: (77.064, 110.526, 125.736, 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 52 16.00 O 1477 8.00 N 1374 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.4 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 36.7% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'R' and resid 27 through 47 removed outlier: 3.924A pdb=" N GLY R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.859A pdb=" N GLU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 removed outlier: 3.933A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 139 Processing helix chain 'R' and resid 141 through 147 Processing helix chain 'R' and resid 150 through 173 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 155 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 157 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.556A pdb=" N LEU R 170 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Proline residue: R 171 - end of helix Processing helix chain 'R' and resid 196 through 227 Processing helix chain 'R' and resid 259 through 276 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 291 through 294 No H-bonds generated for 'chain 'R' and resid 291 through 294' Processing helix chain 'R' and resid 297 through 316 removed outlier: 3.821A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 305 " --> pdb=" O LEU R 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.663A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.543A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.899A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 4.001A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.056A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 178 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.091A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.873A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.929A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.615A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.931A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 999 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: 2.48 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2222 1.44 - 1.57: 4495 1.57 - 1.70: 2 1.70 - 1.83: 74 Bond restraints: 8086 Sorted by residual: bond pdb=" C8 P2E R 401 " pdb=" C9 P2E R 401 " ideal model delta sigma weight residual 1.515 1.436 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C11 P2E R 401 " pdb=" O4 P2E R 401 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 P2E R 401 " pdb=" C11 P2E R 401 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.529 1.576 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C12 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.538 1.498 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8081 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 182 106.64 - 113.50: 4432 113.50 - 120.36: 3089 120.36 - 127.21: 3179 127.21 - 134.07: 81 Bond angle restraints: 10963 Sorted by residual: angle pdb=" N VAL R 156 " pdb=" CA VAL R 156 " pdb=" C VAL R 156 " ideal model delta sigma weight residual 110.62 116.74 -6.12 1.02e+00 9.61e-01 3.59e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C4 P2E R 401 " pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " ideal model delta sigma weight residual 127.52 112.65 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " pdb=" C7 P2E R 401 " ideal model delta sigma weight residual 125.83 111.98 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.71 116.83 -5.12 1.15e+00 7.56e-01 1.98e+01 ... (remaining 10958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4337 16.25 - 32.49: 395 32.49 - 48.74: 83 48.74 - 64.98: 17 64.98 - 81.23: 9 Dihedral angle restraints: 4841 sinusoidal: 1870 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -4.97 -81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.119: 206 0.119 - 0.178: 19 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C15 P2E R 401 " pdb=" C14 P2E R 401 " pdb=" C16 P2E R 401 " pdb=" O5 P2E R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.52 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 P2E R 401 " pdb=" C12 P2E R 401 " pdb=" C7 P2E R 401 " pdb=" C9 P2E R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 390 " pdb=" N GLN A 390 " pdb=" C GLN A 390 " pdb=" CB GLN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1249 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " -0.269 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C13 P2E R 401 " 0.249 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " 0.296 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 388 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.028 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C5 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " -0.028 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 45 2.58 - 3.16: 6354 3.16 - 3.74: 11864 3.74 - 4.32: 17380 4.32 - 4.90: 28736 Nonbonded interactions: 64379 Sorted by model distance: nonbonded pdb=" O ILE A 56 " pdb=" N MET A 60 " model vdw 1.994 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 2.440 nonbonded pdb=" OG1 THR R 82 " pdb=" O HOH R 501 " model vdw 2.133 2.440 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.247 2.520 nonbonded pdb=" O GLU A 50 " pdb=" NH2 ARG A 265 " model vdw 2.276 2.520 ... (remaining 64374 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: 0.590 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: 0.010 Extract box with map and model: 1.920 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8086 Z= 0.281 Angle : 0.712 14.865 10963 Z= 0.396 Chirality : 0.047 0.297 1252 Planarity : 0.009 0.273 1402 Dihedral : 13.642 81.229 2908 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.23), residues: 1002 helix: -0.55 (0.24), residues: 371 sheet: -0.79 (0.32), residues: 210 loop : -2.51 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.024 0.002 TYR B 59 ARG 0.007 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7395 (t80) cc_final: 0.6912 (t80) REVERT: R 116 MET cc_start: 0.7244 (tpp) cc_final: 0.6897 (tpp) REVERT: R 124 MET cc_start: 0.8306 (tpp) cc_final: 0.8033 (tpt) REVERT: R 126 MET cc_start: 0.8307 (tpt) cc_final: 0.8107 (tpt) REVERT: R 282 ILE cc_start: 0.8561 (tt) cc_final: 0.8311 (pt) REVERT: A 20 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6757 (tpp80) REVERT: A 24 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7567 (ttmm) REVERT: B 23 LYS cc_start: 0.8989 (tttp) cc_final: 0.8746 (ttpp) REVERT: B 32 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8284 (tp-100) REVERT: N 12 VAL cc_start: 0.9235 (p) cc_final: 0.9015 (m) REVERT: N 105 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7787 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 1.3661 time to fit residues: 247.1360 Evaluate side-chains 124 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 213 GLN A 390 GLN B 17 GLN B 175 GLN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 77 ASN N 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8086 Z= 0.156 Angle : 0.520 10.056 10963 Z= 0.263 Chirality : 0.041 0.145 1252 Planarity : 0.004 0.053 1402 Dihedral : 5.201 44.689 1140 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.67 % Allowed : 13.23 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1002 helix: 0.95 (0.27), residues: 385 sheet: -0.35 (0.33), residues: 216 loop : -1.99 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 119 TYR 0.010 0.001 TYR B 124 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: R 124 MET cc_start: 0.8273 (tpp) cc_final: 0.8069 (tpt) REVERT: A 20 ARG cc_start: 0.6934 (mtp85) cc_final: 0.6622 (tpp80) REVERT: A 24 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7472 (ttmm) REVERT: B 23 LYS cc_start: 0.8923 (tttp) cc_final: 0.8661 (ttpp) REVERT: B 32 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8242 (tp-100) REVERT: B 217 MET cc_start: 0.7688 (ptm) cc_final: 0.7378 (pp-130) REVERT: N 73 ASP cc_start: 0.7035 (t70) cc_final: 0.6755 (p0) outliers start: 14 outliers final: 6 residues processed: 155 average time/residue: 1.3628 time to fit residues: 222.3882 Evaluate side-chains 131 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN B 17 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8086 Z= 0.202 Angle : 0.522 9.651 10963 Z= 0.265 Chirality : 0.041 0.147 1252 Planarity : 0.004 0.053 1402 Dihedral : 5.208 54.577 1140 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.62 % Allowed : 15.02 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1002 helix: 1.41 (0.27), residues: 387 sheet: -0.14 (0.33), residues: 216 loop : -1.64 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR B 105 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: R 116 MET cc_start: 0.7346 (tpp) cc_final: 0.6749 (tpp) REVERT: A 24 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7531 (ttmm) REVERT: B 19 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7623 (ttm110) REVERT: B 23 LYS cc_start: 0.8971 (tttp) cc_final: 0.8698 (ttpp) REVERT: B 32 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8231 (tp-100) REVERT: B 214 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7350 (mpt180) outliers start: 22 outliers final: 6 residues processed: 143 average time/residue: 1.3791 time to fit residues: 207.3631 Evaluate side-chains 128 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8086 Z= 0.173 Angle : 0.518 9.856 10963 Z= 0.260 Chirality : 0.041 0.146 1252 Planarity : 0.004 0.053 1402 Dihedral : 4.806 57.883 1140 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.62 % Allowed : 16.45 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1002 helix: 1.69 (0.28), residues: 385 sheet: -0.05 (0.33), residues: 222 loop : -1.44 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR R 161 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7252 (t80) cc_final: 0.6873 (t80) REVERT: R 116 MET cc_start: 0.7251 (tpp) cc_final: 0.6676 (tpt) REVERT: R 282 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 24 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7551 (ttmm) REVERT: A 356 ARG cc_start: 0.7776 (pmm-80) cc_final: 0.7556 (ptp-170) REVERT: B 19 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7649 (ttm110) REVERT: B 23 LYS cc_start: 0.8975 (tttp) cc_final: 0.8665 (ttpp) REVERT: B 32 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8245 (tp-100) outliers start: 22 outliers final: 11 residues processed: 146 average time/residue: 1.3433 time to fit residues: 206.5110 Evaluate side-chains 137 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.006 0.049 8086 Z= 0.373 Angle : 0.597 9.385 10963 Z= 0.306 Chirality : 0.044 0.155 1252 Planarity : 0.004 0.046 1402 Dihedral : 5.085 56.052 1140 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.10 % Allowed : 18.12 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1002 helix: 1.70 (0.27), residues: 387 sheet: -0.15 (0.33), residues: 224 loop : -1.37 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.032 0.002 PHE R 119 TYR 0.018 0.002 TYR B 105 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7375 (t80) cc_final: 0.6968 (t80) REVERT: R 116 MET cc_start: 0.7248 (tpp) cc_final: 0.6691 (tpt) REVERT: R 282 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 24 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7612 (ttmm) REVERT: B 19 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7677 (ttm110) REVERT: B 23 LYS cc_start: 0.8959 (tttp) cc_final: 0.8668 (ttpp) REVERT: B 32 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8382 (tp-100) REVERT: B 214 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7482 (mpt180) REVERT: B 260 GLU cc_start: 0.8266 (pt0) cc_final: 0.8062 (pt0) REVERT: B 271 CYS cc_start: 0.8272 (p) cc_final: 0.7767 (p) outliers start: 26 outliers final: 13 residues processed: 143 average time/residue: 1.4185 time to fit residues: 213.2313 Evaluate side-chains 136 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 0.0060 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8086 Z= 0.151 Angle : 0.499 8.642 10963 Z= 0.253 Chirality : 0.040 0.144 1252 Planarity : 0.004 0.046 1402 Dihedral : 4.483 46.819 1140 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.74 % Allowed : 19.19 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1002 helix: 2.06 (0.28), residues: 384 sheet: 0.07 (0.33), residues: 222 loop : -1.31 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.032 0.001 PHE R 119 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7429 (t80) cc_final: 0.7073 (t80) REVERT: R 116 MET cc_start: 0.7217 (tpp) cc_final: 0.6697 (tpt) REVERT: A 24 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7549 (ttmm) REVERT: A 228 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8155 (mtp180) REVERT: A 356 ARG cc_start: 0.7848 (pmm-80) cc_final: 0.7642 (ptp-170) REVERT: B 19 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7641 (ttm110) REVERT: B 23 LYS cc_start: 0.8903 (tttp) cc_final: 0.8609 (ttpp) REVERT: B 32 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8424 (tp-100) REVERT: B 214 ARG cc_start: 0.7741 (mpt180) cc_final: 0.7368 (mpt180) REVERT: B 260 GLU cc_start: 0.8234 (pt0) cc_final: 0.8006 (pt0) REVERT: B 271 CYS cc_start: 0.8159 (p) cc_final: 0.7653 (p) outliers start: 23 outliers final: 7 residues processed: 147 average time/residue: 1.3380 time to fit residues: 207.2386 Evaluate side-chains 138 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8086 Z= 0.152 Angle : 0.498 8.402 10963 Z= 0.253 Chirality : 0.040 0.144 1252 Planarity : 0.004 0.045 1402 Dihedral : 4.293 39.208 1140 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.62 % Allowed : 20.38 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1002 helix: 2.22 (0.28), residues: 377 sheet: 0.12 (0.33), residues: 222 loop : -1.15 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 118 TYR 0.008 0.001 TYR B 124 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7463 (t80) cc_final: 0.7141 (t80) REVERT: R 116 MET cc_start: 0.7220 (tpp) cc_final: 0.6719 (tpt) REVERT: A 24 LYS cc_start: 0.7816 (ttpp) cc_final: 0.7544 (ttmm) REVERT: A 228 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8057 (mtp85) REVERT: B 19 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7636 (ttm110) REVERT: B 23 LYS cc_start: 0.8904 (tttp) cc_final: 0.8608 (ttpp) REVERT: B 32 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8374 (tp-100) REVERT: B 214 ARG cc_start: 0.7827 (mpt180) cc_final: 0.7477 (mpt180) REVERT: B 234 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8135 (m-80) outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 1.3685 time to fit residues: 210.5005 Evaluate side-chains 137 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8086 Z= 0.162 Angle : 0.502 8.157 10963 Z= 0.258 Chirality : 0.040 0.148 1252 Planarity : 0.004 0.045 1402 Dihedral : 4.197 32.219 1140 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.15 % Allowed : 21.10 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1002 helix: 2.26 (0.28), residues: 378 sheet: 0.16 (0.33), residues: 222 loop : -1.09 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE R 118 TYR 0.011 0.001 TYR R 161 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7361 (t80) cc_final: 0.7059 (t80) REVERT: R 116 MET cc_start: 0.7279 (tpp) cc_final: 0.6779 (tpt) REVERT: A 24 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7543 (ttmm) REVERT: A 228 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8080 (mtp85) REVERT: A 356 ARG cc_start: 0.7776 (pmm-80) cc_final: 0.7572 (ptp-170) REVERT: B 19 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7634 (ttm110) REVERT: B 23 LYS cc_start: 0.8913 (tttp) cc_final: 0.8611 (ttpp) REVERT: B 32 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8390 (tp-100) REVERT: B 214 ARG cc_start: 0.7836 (mpt180) cc_final: 0.7459 (mpt180) REVERT: B 234 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8127 (m-80) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 1.3919 time to fit residues: 204.9435 Evaluate side-chains 137 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8086 Z= 0.165 Angle : 0.510 11.260 10963 Z= 0.257 Chirality : 0.040 0.148 1252 Planarity : 0.004 0.046 1402 Dihedral : 4.165 28.531 1140 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.15 % Allowed : 21.45 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1002 helix: 2.27 (0.28), residues: 378 sheet: 0.16 (0.33), residues: 223 loop : -1.05 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 118 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7451 (t80) cc_final: 0.7137 (t80) REVERT: R 116 MET cc_start: 0.7284 (tpp) cc_final: 0.6800 (tpt) REVERT: A 24 LYS cc_start: 0.7812 (ttpp) cc_final: 0.7531 (ttmm) REVERT: A 228 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8153 (mtp180) REVERT: B 19 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7633 (ttm110) REVERT: B 23 LYS cc_start: 0.8911 (tttp) cc_final: 0.8608 (ttpp) REVERT: B 32 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8379 (tp-100) REVERT: B 214 ARG cc_start: 0.7829 (mpt180) cc_final: 0.7509 (mpt180) REVERT: B 234 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: N 89 GLU cc_start: 0.8601 (mp0) cc_final: 0.8310 (mp0) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 1.4289 time to fit residues: 205.6539 Evaluate side-chains 134 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8086 Z= 0.140 Angle : 0.505 11.025 10963 Z= 0.254 Chirality : 0.039 0.145 1252 Planarity : 0.004 0.047 1402 Dihedral : 3.997 26.965 1140 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.79 % Allowed : 21.93 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1002 helix: 2.31 (0.28), residues: 378 sheet: 0.23 (0.33), residues: 223 loop : -1.04 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.028 0.001 PHE R 119 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7465 (t80) cc_final: 0.7146 (t80) REVERT: R 80 LEU cc_start: 0.7951 (tt) cc_final: 0.7663 (tt) REVERT: R 116 MET cc_start: 0.7294 (tpp) cc_final: 0.6800 (tpt) REVERT: A 24 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7512 (ttmm) REVERT: A 228 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8002 (mtp85) REVERT: B 19 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7650 (ttm110) REVERT: B 23 LYS cc_start: 0.8901 (tttp) cc_final: 0.8597 (ttpp) REVERT: B 32 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8364 (tp40) REVERT: B 214 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7500 (mpt180) REVERT: B 234 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: N 89 GLU cc_start: 0.8556 (mp0) cc_final: 0.8279 (mp0) outliers start: 15 outliers final: 11 residues processed: 144 average time/residue: 1.4046 time to fit residues: 212.4800 Evaluate side-chains 139 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105671 restraints weight = 9732.750| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.61 r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8086 Z= 0.174 Angle : 0.514 11.032 10963 Z= 0.257 Chirality : 0.040 0.148 1252 Planarity : 0.004 0.047 1402 Dihedral : 4.066 27.577 1140 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.91 % Allowed : 22.05 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1002 helix: 2.30 (0.28), residues: 378 sheet: 0.24 (0.33), residues: 223 loop : -1.01 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 266 PHE 0.021 0.001 PHE R 119 TYR 0.011 0.001 TYR N 60 ARG 0.008 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3802.49 seconds wall clock time: 67 minutes 48.69 seconds (4068.69 seconds total)