Starting phenix.real_space_refine on Fri Jun 28 14:34:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/06_2024/8x7a_38096_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/06_2024/8x7a_38096.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/06_2024/8x7a_38096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/06_2024/8x7a_38096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/06_2024/8x7a_38096_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/06_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-5370/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: 7.26, per 1000 atoms: 0.46 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: 11.18 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: 2.30 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: 5.48 Time building geometry restraints manager: 11.84 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 1.393 1.670 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C19 Y9J R 401 " pdb=" C20 Y9J R 401 " ideal model delta sigma weight residual 1.389 1.209 0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C18 Y9J R 401 " pdb=" C19 Y9J R 401 " ideal model delta sigma weight residual 1.394 1.215 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" CA MET R 244 " pdb=" C MET R 244 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.50e+01 ... (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 121.72 143.69 -21.97 3.00e+00 1.11e-01 5.36e+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 - 21.03: 7234 21.03 - 42.07: 193 42.07 - 63.10: 73 63.10 - 84.14: 10 84.14 - 105.17: 1 Dihedral angle restraints: 7511 sinusoidal: 3974 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 7508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1158 0.074 - 0.149: 86 0.149 - 0.223: 5 0.223 - 0.298: 1 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=" 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 chirality pdb=" C13 Y9J R 401 " pdb=" C12 Y9J R 401 " pdb=" C14 Y9J R 401 " pdb=" C9 Y9J R 401 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.05e+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: 2.840 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: 0.210 Extract box with map and model: 7.350 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 49.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.730 ------------------------------------------------------------------------------- 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 : 0.019 1.639 8108 Z= 1.691 Angle : 0.993 62.660 11001 Z= 0.688 Chirality : 0.040 0.372 1251 Planarity : 0.006 0.190 1419 Dihedral : 8.424 105.175 2894 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 : 1.150 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: 2.2619 time to fit residues: 753.5575 Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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: N 5 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8108 Z= 0.188 Angle : 0.547 6.405 11001 Z= 0.282 Chirality : 0.038 0.147 1251 Planarity : 0.005 0.054 1419 Dihedral : 4.724 68.204 1171 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.14 % Favored : 97.77 % Rotamer: Outliers : 2.85 % Allowed : 20.67 % Favored : 76.49 % 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: 0.54 (0.27), residues: 1030 helix: 2.03 (0.27), residues: 398 sheet: -0.50 (0.31), residues: 243 loop : -0.79 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 237 PHE 0.008 0.001 PHE N 68 TYR 0.015 0.001 TYR A 37 ARG 0.008 0.001 ARG A 273 *********************** 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 199 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.015 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: R 41 ARG cc_start: 0.6649 (ptm-80) cc_final: 0.6395 (mmt-90) outliers start: 23 outliers final: 12 residues processed: 190 average time/residue: 1.8622 time to fit residues: 381.7759 Evaluate side-chains 167 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 42 GLU Chi-restraints excluded: chain G residue 57 SER 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: 0.4980 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 62 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8108 Z= 0.174 Angle : 0.527 6.658 11001 Z= 0.268 Chirality : 0.038 0.155 1251 Planarity : 0.004 0.059 1419 Dihedral : 4.656 69.002 1171 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.34 % Allowed : 20.05 % Favored : 76.61 % 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: 0.87 (0.27), residues: 1030 helix: 2.29 (0.27), residues: 399 sheet: -0.29 (0.32), residues: 237 loop : -0.62 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 220 PHE 0.014 0.001 PHE R 102 TYR 0.016 0.001 TYR A 37 ARG 0.006 0.000 ARG R 219 *********************** 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 187 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.265 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: R 86 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.4186 (mtm180) outliers start: 27 outliers final: 13 residues processed: 175 average time/residue: 2.0438 time to fit residues: 384.6724 Evaluate side-chains 155 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 N residue 18 LEU Chi-restraints excluded: chain N residue 63 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 207 THR Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 overall best weight: 1.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8108 Z= 0.255 Angle : 0.552 6.723 11001 Z= 0.285 Chirality : 0.039 0.149 1251 Planarity : 0.004 0.044 1419 Dihedral : 4.888 68.795 1171 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.47 % Allowed : 21.04 % Favored : 75.50 % 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: 1.10 (0.27), residues: 1030 helix: 2.44 (0.27), residues: 400 sheet: -0.36 (0.31), residues: 253 loop : -0.29 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.009 0.001 HIS R 237 PHE 0.012 0.001 PHE R 102 TYR 0.016 0.001 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 175 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.352 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: 0.5910 (OUTLIER) cc_final: 0.4185 (mtm180) outliers start: 28 outliers final: 13 residues processed: 162 average time/residue: 1.7752 time to fit residues: 311.7218 Evaluate side-chains 148 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 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 148 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8108 Z= 0.165 Angle : 0.511 5.066 11001 Z= 0.260 Chirality : 0.038 0.151 1251 Planarity : 0.004 0.049 1419 Dihedral : 4.673 66.520 1171 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.48 % Allowed : 21.29 % Favored : 76.24 % 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: 1.27 (0.27), residues: 1030 helix: 2.63 (0.27), residues: 400 sheet: -0.25 (0.32), residues: 245 loop : -0.29 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.008 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.014 0.001 TYR N 60 ARG 0.012 0.001 ARG G 13 *********************** 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 166 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.224 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: R 86 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.4208 (mtm180) REVERT: R 274 ASP cc_start: 0.7726 (m-30) cc_final: 0.7476 (m-30) outliers start: 20 outliers final: 13 residues processed: 159 average time/residue: 1.7426 time to fit residues: 300.3796 Evaluate side-chains 143 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain B residue 316 SER 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 207 THR Chi-restraints excluded: chain R residue 220 HIS 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: 9.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8108 Z= 0.332 Angle : 0.594 7.212 11001 Z= 0.311 Chirality : 0.040 0.166 1251 Planarity : 0.004 0.042 1419 Dihedral : 5.182 67.552 1171 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.97 % Allowed : 21.16 % Favored : 75.87 % 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: 0.99 (0.27), residues: 1030 helix: 2.39 (0.27), residues: 401 sheet: -0.39 (0.32), residues: 251 loop : -0.42 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 290 HIS 0.009 0.002 HIS R 237 PHE 0.016 0.002 PHE R 102 TYR 0.017 0.002 TYR R 188 ARG 0.008 0.001 ARG G 13 *********************** 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 153 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.238 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: 0.5936 (OUTLIER) cc_final: 0.4208 (mtm180) REVERT: R 138 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6756 (tt) outliers start: 24 outliers final: 9 residues processed: 146 average time/residue: 1.8108 time to fit residues: 285.7235 Evaluate side-chains 131 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 57 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 252 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8108 Z= 0.242 Angle : 0.554 7.415 11001 Z= 0.285 Chirality : 0.039 0.149 1251 Planarity : 0.004 0.041 1419 Dihedral : 4.963 68.361 1171 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.86 % Allowed : 22.15 % Favored : 75.99 % 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: 1.18 (0.27), residues: 1030 helix: 2.55 (0.27), residues: 402 sheet: -0.24 (0.32), residues: 242 loop : -0.39 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 290 HIS 0.007 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.015 0.002 TYR N 60 ARG 0.007 0.000 ARG G 13 *********************** 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 139 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.008 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: R 86 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.4145 (mtm180) REVERT: R 138 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6747 (tt) outliers start: 15 outliers final: 8 residues processed: 136 average time/residue: 2.0947 time to fit residues: 305.1482 Evaluate side-chains 127 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** 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: 0.7582 moved from start: 0.6708 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= 0.183 Angle : 0.540 7.728 11001 Z= 0.275 Chirality : 0.038 0.145 1251 Planarity : 0.004 0.040 1419 Dihedral : 4.752 67.647 1171 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.61 % Allowed : 22.52 % Favored : 75.87 % 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: 1.40 (0.27), residues: 1030 helix: 2.73 (0.27), residues: 402 sheet: -0.16 (0.34), residues: 225 loop : -0.25 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 290 HIS 0.005 0.001 HIS R 237 PHE 0.017 0.001 PHE R 102 TYR 0.014 0.001 TYR N 60 ARG 0.008 0.000 ARG R 45 *********************** 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 137 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.383 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: 0.5900 (OUTLIER) cc_final: 0.4129 (mtm180) REVERT: R 138 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6736 (tt) outliers start: 13 outliers final: 9 residues processed: 133 average time/residue: 2.0001 time to fit residues: 286.5793 Evaluate side-chains 131 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain N residue 93 VAL 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: 3.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 129 GLN ** 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: 0.7597 moved from start: 0.6795 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= 0.210 Angle : 0.543 9.543 11001 Z= 0.278 Chirality : 0.038 0.150 1251 Planarity : 0.004 0.039 1419 Dihedral : 4.782 67.853 1171 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.36 % Allowed : 23.14 % Favored : 75.50 % 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: 1.40 (0.27), residues: 1030 helix: 2.72 (0.27), residues: 401 sheet: -0.14 (0.34), residues: 225 loop : -0.23 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 290 HIS 0.006 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.016 0.001 TYR R 281 ARG 0.004 0.000 ARG R 302 *********************** 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 136 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.059 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: 0.5913 (OUTLIER) cc_final: 0.4143 (mtm180) REVERT: R 138 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6744 (tt) outliers start: 11 outliers final: 7 residues processed: 134 average time/residue: 1.9693 time to fit residues: 283.9783 Evaluate side-chains 129 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 N residue 93 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8108 Z= 0.341 Angle : 0.603 9.801 11001 Z= 0.312 Chirality : 0.039 0.149 1251 Planarity : 0.004 0.042 1419 Dihedral : 5.142 69.705 1171 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.11 % Allowed : 23.64 % Favored : 75.25 % 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: 1.22 (0.27), residues: 1030 helix: 2.53 (0.27), residues: 401 sheet: -0.22 (0.34), residues: 226 loop : -0.30 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 290 HIS 0.007 0.001 HIS R 237 PHE 0.016 0.002 PHE R 102 TYR 0.019 0.002 TYR R 281 ARG 0.008 0.001 ARG G 13 ********************** 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 130 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.288 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: 0.5945 (OUTLIER) cc_final: 0.4154 (mtm180) REVERT: R 138 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6693 (tt) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 2.1117 time to fit residues: 292.2958 Evaluate side-chains 125 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 N residue 93 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.3882 r_free = 0.3882 target = 0.116622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086081 restraints weight = 48236.744| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.55 r_work: 0.3229 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.7013 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= 0.166 Angle : 0.555 9.947 11001 Z= 0.280 Chirality : 0.038 0.139 1251 Planarity : 0.004 0.040 1419 Dihedral : 4.803 68.487 1171 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.36 % Allowed : 23.51 % 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: 1.41 (0.27), residues: 1030 helix: 2.74 (0.27), residues: 401 sheet: -0.09 (0.35), residues: 209 loop : -0.27 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 290 HIS 0.004 0.001 HIS R 237 PHE 0.020 0.001 PHE R 102 TYR 0.014 0.001 TYR N 60 ARG 0.011 0.001 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6736.89 seconds wall clock time: 116 minutes 18.33 seconds (6978.33 seconds total)