Starting phenix.real_space_refine on Tue Apr 9 06:38:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/04_2024/8x7a_38096_neut_trim_updated.pdb" } resolution = 2.56 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= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 5028 2.51 5 N 1399 2.21 5 O 1466 1.98 5 H 7679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 364": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15628 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3761 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 4782 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 851 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1849 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4357 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y9J': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.94, per 1000 atoms: 0.44 Number of scatterers: 15628 At special positions: 0 Unit cell: (81.03, 106.58, 128.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1466 8.00 N 1399 7.00 C 5028 6.00 H 7679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 12.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 37.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.910A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.804A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 382 removed outlier: 3.692A pdb=" N ALA A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 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 7 through 23 removed outlier: 3.502A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 19 through 40 removed outlier: 3.608A pdb=" N GLY R 27 " --> pdb=" O MET R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 77 removed outlier: 3.605A pdb=" N THR R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU R 67 " --> pdb=" O GLY R 63 " (cutoff:3.500A) Proline residue: R 69 - end of helix Processing helix chain 'R' and resid 92 through 122 Processing helix chain 'R' and resid 124 through 128 Processing helix chain 'R' and resid 132 through 152 Proline residue: R 141 - end of helix removed outlier: 3.726A pdb=" N ALA R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 156 No H-bonds generated for 'chain 'R' and resid 154 through 156' Processing helix chain 'R' and resid 184 through 220 Processing helix chain 'R' and resid 233 through 263 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 272 through 282 Processing helix chain 'R' and resid 284 through 291 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 297 through 312 removed outlier: 4.634A pdb=" N CYS R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU R 310 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.354A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.268A 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: 6.713A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.679A 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: 6.440A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.524A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.759A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 17 through 22 Processing sheet with id= K, first strand: chain 'N' and resid 49 through 51 removed outlier: 3.999A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 161 through 163 364 hydrogen bonds defined for protein. 990 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: 5.58 Time building geometry restraints manager: 13.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.25: 8967 1.25 - 1.68: 6741 1.68 - 2.11: 78 2.11 - 2.54: 0 2.54 - 2.97: 1 Bond restraints: 15787 Sorted by residual: bond pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 1.332 2.972 -1.639 1.40e-02 5.10e+03 1.37e+04 bond pdb=" C15 Y9J R 401 " pdb=" C21 Y9J R 401 " ideal model delta sigma weight residual 1.385 1.670 -0.285 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C13 Y9J R 401 " pdb=" C9 Y9J R 401 " ideal model delta sigma weight residual 1.270 1.483 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C19 Y9J R 401 " pdb=" C20 Y9J R 401 " ideal model delta sigma weight residual 1.422 1.209 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C11 Y9J R 401 " pdb=" C12 Y9J R 401 " ideal model delta sigma weight residual 1.336 1.547 -0.211 2.00e-02 2.50e+03 1.12e+02 ... (remaining 15782 not shown) Histogram of bond angle deviations from ideal: 59.61 - 77.69: 2 77.69 - 95.77: 0 95.77 - 113.85: 18591 113.85 - 131.93: 9745 131.93 - 150.01: 20 Bond angle restraints: 28358 Sorted by residual: angle pdb=" O ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 122.27 59.61 62.66 1.16e+00 7.43e-01 2.92e+03 angle pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 118.79 150.01 -31.22 1.22e+00 6.72e-01 6.55e+02 angle pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" H ASP B 205 " ideal model delta sigma weight residual 124.38 66.43 57.95 3.00e+00 1.11e-01 3.73e+02 angle pdb=" C14 Y9J R 401 " pdb=" C15 Y9J R 401 " pdb=" C21 Y9J R 401 " ideal model delta sigma weight residual 119.49 143.69 -24.20 3.00e+00 1.11e-01 6.50e+01 angle pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta sigma weight residual 121.54 135.26 -13.72 1.91e+00 2.74e-01 5.16e+01 ... (remaining 28353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 7234 22.72 - 45.43: 183 45.43 - 68.15: 63 68.15 - 90.86: 6 90.86 - 113.58: 3 Dihedral angle restraints: 7489 sinusoidal: 3952 harmonic: 3537 Sorted by residual: dihedral pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual -180.00 -74.83 -105.17 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" C MET R 244 " pdb=" N MET R 244 " pdb=" CA MET R 244 " pdb=" CB MET R 244 " ideal model delta harmonic sigma weight residual -122.60 -110.06 -12.54 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ALA R 265 " pdb=" N ALA R 265 " pdb=" CA ALA R 265 " pdb=" CB ALA R 265 " ideal model delta harmonic sigma weight residual -122.60 -134.35 11.75 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1156 0.074 - 0.149: 89 0.149 - 0.223: 3 0.223 - 0.298: 2 0.298 - 0.372: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CA ALA R 265 " pdb=" N ALA R 265 " pdb=" C ALA R 265 " pdb=" CB ALA R 265 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C12 Y9J R 401 " pdb=" C11 Y9J R 401 " pdb=" C13 Y9J R 401 " pdb=" C17 Y9J R 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.84 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA VAL R 25 " pdb=" N VAL R 25 " pdb=" C VAL R 25 " pdb=" CB VAL R 25 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1248 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 203 " 0.036 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" N ASP B 205 " -0.362 2.00e-02 2.50e+03 pdb=" CA ASP B 205 " 0.141 2.00e-02 2.50e+03 pdb=" H ASP B 205 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 203 " 0.182 2.00e-02 2.50e+03 1.90e-01 3.60e+02 pdb=" C ALA B 203 " -0.318 2.00e-02 2.50e+03 pdb=" O ALA B 203 " 0.062 2.00e-02 2.50e+03 pdb=" N ASP B 205 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 84 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU R 84 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU R 84 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 85 " 0.024 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 886 2.21 - 2.80: 32569 2.80 - 3.40: 42910 3.40 - 4.00: 55126 4.00 - 4.60: 86091 Nonbonded interactions: 217582 Sorted by model distance: nonbonded pdb=" O SER B 189 " pdb=" HG SER B 201 " model vdw 1.607 1.850 nonbonded pdb=" H THR B 221 " pdb=" OE2 GLU G 22 " model vdw 1.609 1.850 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.625 1.850 nonbonded pdb="HD21 ASN R 203 " pdb=" OG1 THR R 245 " model vdw 1.633 1.850 nonbonded pdb=" O LYS N 33 " pdb=" H CYS N 99 " model vdw 1.645 1.850 ... (remaining 217577 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: 3.610 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: 7.130 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 52.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.020 1.639 8108 Z= 1.712 Angle : 0.946 62.660 11001 Z= 0.681 Chirality : 0.040 0.372 1251 Planarity : 0.006 0.190 1419 Dihedral : 8.976 113.580 2872 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Cbeta Deviations : 0.21 % 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: -0.63 (0.25), residues: 1028 helix: 0.95 (0.25), residues: 394 sheet: -0.65 (0.32), residues: 210 loop : -1.59 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 271 HIS 0.002 0.000 HIS B 142 PHE 0.005 0.001 PHE R 24 TYR 0.023 0.001 TYR R 75 ARG 0.002 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 2.3666 time to fit residues: 787.9384 Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN N 5 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8108 Z= 0.195 Angle : 0.539 5.866 11001 Z= 0.279 Chirality : 0.038 0.154 1251 Planarity : 0.005 0.055 1419 Dihedral : 7.033 100.117 1149 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.04 % Favored : 97.86 % Rotamer: Outliers : 2.72 % Allowed : 20.92 % Favored : 76.36 % 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: 0.55 (0.27), residues: 1030 helix: 2.06 (0.27), residues: 398 sheet: -0.50 (0.31), residues: 243 loop : -0.80 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS A 41 PHE 0.008 0.001 PHE R 102 TYR 0.015 0.001 TYR A 37 ARG 0.007 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 ARG cc_start: 0.6641 (ptm-80) cc_final: 0.6388 (mmt-90) outliers start: 22 outliers final: 12 residues processed: 190 average time/residue: 1.9785 time to fit residues: 405.3231 Evaluate side-chains 166 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8108 Z= 0.270 Angle : 0.567 6.475 11001 Z= 0.297 Chirality : 0.039 0.152 1251 Planarity : 0.005 0.057 1419 Dihedral : 6.880 99.802 1149 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.84 % Allowed : 19.43 % Favored : 76.73 % 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: 0.88 (0.26), residues: 1030 helix: 2.25 (0.27), residues: 400 sheet: -0.45 (0.31), residues: 253 loop : -0.42 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.019 0.002 TYR A 37 ARG 0.020 0.001 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.4201 (mtm180) outliers start: 31 outliers final: 15 residues processed: 177 average time/residue: 2.0046 time to fit residues: 382.1588 Evaluate side-chains 151 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 300 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 88 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8108 Z= 0.284 Angle : 0.571 7.071 11001 Z= 0.297 Chirality : 0.039 0.151 1251 Planarity : 0.004 0.050 1419 Dihedral : 6.349 62.325 1149 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.59 % Allowed : 20.05 % Favored : 76.36 % 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: 0.96 (0.27), residues: 1030 helix: 2.36 (0.27), residues: 400 sheet: -0.44 (0.31), residues: 253 loop : -0.41 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.016 0.002 TYR A 37 ARG 0.008 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.4212 (mtm180) REVERT: R 174 MET cc_start: 0.6644 (ptp) cc_final: 0.6332 (ptp) REVERT: R 274 ASP cc_start: 0.7741 (m-30) cc_final: 0.7417 (m-30) REVERT: R 281 TYR cc_start: 0.8366 (t80) cc_final: 0.8023 (t80) outliers start: 29 outliers final: 14 residues processed: 157 average time/residue: 1.9270 time to fit residues: 327.4934 Evaluate side-chains 147 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 267 ASP Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0670 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8108 Z= 0.185 Angle : 0.527 6.581 11001 Z= 0.270 Chirality : 0.038 0.147 1251 Planarity : 0.004 0.039 1419 Dihedral : 5.915 55.720 1149 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.60 % Allowed : 21.04 % Favored : 76.36 % 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: 1.17 (0.27), residues: 1030 helix: 2.56 (0.27), residues: 402 sheet: -0.28 (0.32), residues: 249 loop : -0.39 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.007 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.014 0.001 TYR A 37 ARG 0.006 0.000 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.4219 (mtm180) REVERT: R 281 TYR cc_start: 0.8313 (t80) cc_final: 0.8010 (t80) outliers start: 21 outliers final: 12 residues processed: 153 average time/residue: 1.9474 time to fit residues: 322.6998 Evaluate side-chains 147 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8108 Z= 0.261 Angle : 0.549 7.142 11001 Z= 0.284 Chirality : 0.038 0.150 1251 Planarity : 0.004 0.075 1419 Dihedral : 5.871 55.085 1149 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.72 % Allowed : 21.66 % Favored : 75.62 % 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: 1.21 (0.27), residues: 1030 helix: 2.62 (0.27), residues: 402 sheet: -0.29 (0.32), residues: 249 loop : -0.38 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.008 0.001 HIS R 237 PHE 0.015 0.001 PHE R 102 TYR 0.014 0.001 TYR A 37 ARG 0.016 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.4221 (mtm180) outliers start: 22 outliers final: 12 residues processed: 147 average time/residue: 2.1663 time to fit residues: 347.6716 Evaluate side-chains 140 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 234 GLU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN R 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8108 Z= 0.211 Angle : 0.550 8.646 11001 Z= 0.281 Chirality : 0.038 0.152 1251 Planarity : 0.004 0.050 1419 Dihedral : 5.682 53.551 1149 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.98 % Allowed : 22.90 % Favored : 75.12 % 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: 1.31 (0.27), residues: 1030 helix: 2.64 (0.27), residues: 402 sheet: -0.17 (0.33), residues: 232 loop : -0.28 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.013 0.001 TYR A 37 ARG 0.010 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.4128 (mtm180) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 2.3098 time to fit residues: 360.2519 Evaluate side-chains 135 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8108 Z= 0.181 Angle : 0.548 8.761 11001 Z= 0.277 Chirality : 0.038 0.158 1251 Planarity : 0.004 0.051 1419 Dihedral : 5.611 56.976 1149 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.49 % Allowed : 23.89 % Favored : 74.63 % 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: 1.45 (0.27), residues: 1030 helix: 2.74 (0.27), residues: 402 sheet: -0.10 (0.33), residues: 232 loop : -0.21 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.014 0.001 TYR R 281 ARG 0.009 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.4140 (mtm180) REVERT: R 138 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6704 (tt) outliers start: 12 outliers final: 8 residues processed: 134 average time/residue: 2.1813 time to fit residues: 313.3774 Evaluate side-chains 136 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8108 Z= 0.270 Angle : 0.574 9.333 11001 Z= 0.296 Chirality : 0.039 0.152 1251 Planarity : 0.004 0.039 1419 Dihedral : 6.012 73.848 1149 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.98 % Allowed : 22.90 % Favored : 75.12 % 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: 1.34 (0.27), residues: 1030 helix: 2.64 (0.27), residues: 401 sheet: -0.14 (0.33), residues: 232 loop : -0.26 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 290 HIS 0.007 0.001 HIS R 237 PHE 0.013 0.001 PHE R 102 TYR 0.017 0.001 TYR R 281 ARG 0.009 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.4175 (mtm180) REVERT: R 138 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6684 (tt) outliers start: 16 outliers final: 9 residues processed: 136 average time/residue: 2.2841 time to fit residues: 332.0170 Evaluate side-chains 136 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 299 VAL Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 chunk 61 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8108 Z= 0.217 Angle : 0.564 9.625 11001 Z= 0.288 Chirality : 0.038 0.148 1251 Planarity : 0.004 0.048 1419 Dihedral : 5.856 67.003 1149 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.36 % Allowed : 24.26 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 1030 helix: 2.73 (0.27), residues: 401 sheet: -0.07 (0.34), residues: 232 loop : -0.21 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.012 0.001 TYR A 37 ARG 0.008 0.001 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.4146 (mtm180) REVERT: R 138 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6660 (tt) outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 2.3259 time to fit residues: 338.2538 Evaluate side-chains 133 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.116239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085714 restraints weight = 48679.582| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.53 r_work: 0.3231 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8108 Z= 0.197 Angle : 0.559 9.820 11001 Z= 0.284 Chirality : 0.038 0.149 1251 Planarity : 0.004 0.041 1419 Dihedral : 5.743 64.206 1149 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.49 % Allowed : 23.89 % Favored : 74.63 % 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: 1.46 (0.27), residues: 1030 helix: 2.78 (0.27), residues: 400 sheet: 0.11 (0.35), residues: 209 loop : -0.33 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.013 0.001 TYR R 281 ARG 0.008 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7182.67 seconds wall clock time: 128 minutes 1.44 seconds (7681.44 seconds total)