Starting phenix.real_space_refine on Fri Jun 28 18:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x79_38095/06_2024/8x79_38095_neut_trim_updated.pdb" } resolution = 2.41 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= 0.081 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 60 5.16 5 C 5156 2.51 5 N 1447 2.21 5 O 1491 1.98 5 H 7994 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 GLU 15": "OE1" <-> "OE2" 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 GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 289": "OE1" <-> "OE2" 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 GLU 3": "OE1" <-> "OE2" 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 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 215": "OE1" <-> "OE2" 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 GLU 22": "OE1" <-> "OE2" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 58": "OE1" <-> "OE2" 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 GLU 46": "OE1" <-> "OE2" 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 "N ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R GLU 234": "OE1" <-> "OE2" Residue "R ARG 279": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 296": "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: 16148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3820 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 4970 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 870 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1861 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4596 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'Y9Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.02, per 1000 atoms: 0.50 Number of scatterers: 16148 At special positions: 0 Unit cell: (79.57, 102.93, 130.67, 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 60 16.00 O 1491 8.00 N 1447 7.00 C 5156 6.00 H 7994 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: 13.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 11 sheets defined 38.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.994A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.107A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 4.914A 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 284 through 293 Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.646A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 381 removed outlier: 3.661A pdb=" N ALA A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 364 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.612A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 18 through 38 Processing helix chain 'R' and resid 48 through 77 Proline residue: R 69 - end of helix Processing helix chain 'R' and resid 90 through 121 Processing helix chain 'R' and resid 124 through 129 removed outlier: 3.647A pdb=" N GLN R 129 " --> pdb=" O TYR R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 156 Proline residue: R 141 - end of helix removed outlier: 3.547A pdb=" N LEU R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Proline residue: R 154 - end of helix Processing helix chain 'R' and resid 179 through 220 removed outlier: 5.266A pdb=" N PHE R 184 " --> pdb=" O GLY R 180 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER R 185 " --> pdb=" O GLY R 181 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG R 219 " --> pdb=" O ARG R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 265 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 273 through 293 removed outlier: 3.775A pdb=" N LEU R 276 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN R 284 " --> pdb=" O TYR R 281 " (cutoff:3.500A) Proline residue: R 285 - end of helix removed outlier: 4.011A pdb=" N ASP R 288 " --> pdb=" O PRO R 285 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 297 through 312 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.298A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.902A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.297A 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: 6.757A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.539A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.574A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.125A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.647A 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: 3.995A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.535A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.118A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 161 through 163 385 hydrogen bonds defined for protein. 1029 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: 6.01 Time building geometry restraints manager: 14.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7957 1.02 - 1.22: 42 1.22 - 1.41: 3459 1.41 - 1.61: 4771 1.61 - 1.81: 83 Bond restraints: 16312 Sorted by residual: bond pdb=" SG CYS R 170 " pdb=" HG CYS R 170 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" CA TRP R 169 " pdb=" C TRP R 169 " ideal model delta sigma weight residual 1.521 1.449 0.072 1.21e-02 6.83e+03 3.52e+01 bond pdb=" NE ARG R 279 " pdb=" HE ARG R 279 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" NE ARG R 173 " pdb=" HE ARG R 173 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ASP A 321 " pdb=" CA ASP A 321 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.41e-02 5.03e+03 2.30e+01 ... (remaining 16307 not shown) Histogram of bond angle deviations from ideal: 75.64 - 87.32: 3 87.32 - 99.00: 0 99.00 - 110.67: 16634 110.67 - 122.35: 10270 122.35 - 134.03: 2397 Bond angle restraints: 29304 Sorted by residual: angle pdb=" CB PHE R 171 " pdb=" CA PHE R 171 " pdb=" HA PHE R 171 " ideal model delta sigma weight residual 109.00 75.64 33.36 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C PHE R 171 " pdb=" CA PHE R 171 " pdb=" HA PHE R 171 " ideal model delta sigma weight residual 109.00 76.36 32.64 3.00e+00 1.11e-01 1.18e+02 angle pdb=" N PHE R 171 " pdb=" CA PHE R 171 " pdb=" HA PHE R 171 " ideal model delta sigma weight residual 110.00 80.64 29.36 3.00e+00 1.11e-01 9.58e+01 angle pdb=" N MET R 174 " pdb=" CA MET R 174 " pdb=" C MET R 174 " ideal model delta sigma weight residual 111.69 104.09 7.60 1.23e+00 6.61e-01 3.82e+01 angle pdb=" N PHE R 171 " pdb=" CA PHE R 171 " pdb=" C PHE R 171 " ideal model delta sigma weight residual 109.50 118.15 -8.65 1.58e+00 4.01e-01 3.00e+01 ... (remaining 29299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.98: 7364 28.98 - 57.96: 294 57.96 - 86.94: 37 86.94 - 115.92: 3 115.92 - 144.90: 2 Dihedral angle restraints: 7700 sinusoidal: 4108 harmonic: 3592 Sorted by residual: dihedral pdb=" C PHE R 171 " pdb=" N PHE R 171 " pdb=" CA PHE R 171 " pdb=" CB PHE R 171 " ideal model delta harmonic sigma weight residual -122.60 -138.55 15.95 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" N PHE R 171 " pdb=" C PHE R 171 " pdb=" CA PHE R 171 " pdb=" CB PHE R 171 " ideal model delta harmonic sigma weight residual 122.80 138.43 -15.63 0 2.50e+00 1.60e-01 3.91e+01 dihedral pdb=" C5 Y9Q R 401 " pdb=" C6 Y9Q R 401 " pdb=" C7 Y9Q R 401 " pdb=" O1 Y9Q R 401 " ideal model delta sinusoidal sigma weight residual -178.72 -33.82 -144.90 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1253 0.126 - 0.251: 5 0.251 - 0.377: 1 0.377 - 0.502: 0 0.502 - 0.628: 1 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA PHE R 171 " pdb=" N PHE R 171 " pdb=" C PHE R 171 " pdb=" CB PHE R 171 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.86e+00 chirality pdb=" CA GLU A 320 " pdb=" N GLU A 320 " pdb=" C GLU A 320 " pdb=" CB GLU A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA TRP R 169 " pdb=" N TRP R 169 " pdb=" C TRP R 169 " pdb=" CB TRP R 169 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1257 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 170 " 0.050 2.00e-02 2.50e+03 1.04e-01 1.07e+02 pdb=" N PHE R 171 " -0.178 2.00e-02 2.50e+03 pdb=" CA PHE R 171 " 0.045 2.00e-02 2.50e+03 pdb=" H PHE R 171 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 172 " 0.023 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" N ARG R 173 " -0.078 2.00e-02 2.50e+03 pdb=" CA ARG R 173 " 0.020 2.00e-02 2.50e+03 pdb=" H ARG R 173 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 174 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" N ARG R 175 " 0.064 2.00e-02 2.50e+03 pdb=" CA ARG R 175 " -0.016 2.00e-02 2.50e+03 pdb=" H ARG R 175 " -0.029 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 829 2.19 - 2.79: 32330 2.79 - 3.39: 45037 3.39 - 4.00: 58407 4.00 - 4.60: 90768 Nonbonded interactions: 227371 Sorted by model distance: nonbonded pdb="HG21 VAL N 64 " pdb=" HB2 PHE N 68 " model vdw 1.583 2.440 nonbonded pdb=" HG3 PRO R 166 " pdb=" HE1 TRP R 169 " model vdw 1.607 2.270 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.614 1.850 nonbonded pdb="HD22 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 1.638 1.850 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.656 1.850 ... (remaining 227366 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: 0.010 Normalize map: mean=0, sd=1: 1.910 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: 0.240 Extract box with map and model: 7.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 56.170 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8318 Z= 0.216 Angle : 0.556 11.095 11262 Z= 0.331 Chirality : 0.043 0.628 1260 Planarity : 0.003 0.072 1451 Dihedral : 14.622 144.898 2978 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.30 % Allowed : 12.26 % Favored : 86.44 % Cbeta Deviations : 0.20 % 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: -0.03 (0.26), residues: 1039 helix: 0.88 (0.25), residues: 394 sheet: 0.01 (0.33), residues: 228 loop : -0.83 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 169 HIS 0.002 0.000 HIS R 220 PHE 0.006 0.001 PHE R 184 TYR 0.006 0.001 TYR A 329 ARG 0.010 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 261 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.8316 (mmm) cc_final: 0.7770 (mmm) REVERT: R 38 LEU cc_start: 0.8539 (mt) cc_final: 0.8330 (tp) REVERT: R 168 SER cc_start: 0.7060 (OUTLIER) cc_final: 0.6401 (p) outliers start: 11 outliers final: 3 residues processed: 270 average time/residue: 2.8011 time to fit residues: 796.1525 Evaluate side-chains 146 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 174 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 218 ASN B 13 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8318 Z= 0.269 Angle : 0.541 4.676 11262 Z= 0.289 Chirality : 0.041 0.376 1260 Planarity : 0.005 0.050 1451 Dihedral : 7.393 155.509 1163 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.66 % Allowed : 22.52 % Favored : 73.82 % 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: 0.91 (0.26), residues: 1039 helix: 1.94 (0.26), residues: 398 sheet: 0.01 (0.32), residues: 239 loop : -0.30 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.004 0.001 HIS A 377 PHE 0.010 0.001 PHE B 278 TYR 0.011 0.001 TYR R 214 ARG 0.005 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.325 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: A 35 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: A 64 HIS cc_start: 0.4443 (t-90) cc_final: 0.3873 (t-90) REVERT: B 256 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7857 (mtp85) REVERT: B 303 ASP cc_start: 0.7252 (m-30) cc_final: 0.6953 (m-30) REVERT: R 215 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7270 (ttp-110) REVERT: R 272 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.5582 (ptt) outliers start: 31 outliers final: 9 residues processed: 164 average time/residue: 2.6779 time to fit residues: 464.1469 Evaluate side-chains 132 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 272 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 13 GLN B 88 ASN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8318 Z= 0.230 Angle : 0.510 4.591 11262 Z= 0.269 Chirality : 0.041 0.363 1260 Planarity : 0.004 0.035 1451 Dihedral : 7.054 173.294 1158 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.54 % Allowed : 22.76 % Favored : 73.70 % 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 (0.26), residues: 1039 helix: 2.18 (0.26), residues: 396 sheet: 0.10 (0.32), residues: 243 loop : -0.14 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE A 212 TYR 0.007 0.001 TYR A 329 ARG 0.004 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: A 64 HIS cc_start: 0.4932 (t-90) cc_final: 0.4379 (t-90) REVERT: B 256 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7816 (mtp85) REVERT: R 28 VAL cc_start: 0.8452 (t) cc_final: 0.8246 (m) REVERT: R 215 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7241 (ttp-110) outliers start: 30 outliers final: 13 residues processed: 156 average time/residue: 2.8132 time to fit residues: 466.1618 Evaluate side-chains 130 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.0020 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN R 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8318 Z= 0.326 Angle : 0.559 4.940 11262 Z= 0.298 Chirality : 0.042 0.365 1260 Planarity : 0.005 0.043 1451 Dihedral : 7.330 179.561 1157 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.13 % Allowed : 23.35 % Favored : 72.52 % 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: 1.06 (0.26), residues: 1039 helix: 2.04 (0.26), residues: 397 sheet: 0.02 (0.32), residues: 239 loop : -0.12 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.011 0.002 PHE R 184 TYR 0.009 0.002 TYR A 329 ARG 0.005 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: A 27 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 35 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: A 342 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.8060 (t) REVERT: B 13 GLN cc_start: 0.7399 (tm130) cc_final: 0.7060 (tt0) REVERT: B 256 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7801 (mtp85) REVERT: N 5 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6793 (mp-120) REVERT: R 6 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4213 (mmp-170) REVERT: R 72 PHE cc_start: 0.7763 (m-10) cc_final: 0.7341 (m-10) REVERT: R 215 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7299 (ttp-110) outliers start: 35 outliers final: 15 residues processed: 148 average time/residue: 2.7678 time to fit residues: 433.4537 Evaluate side-chains 138 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 ASP Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 41 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN R 216 GLN R 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8318 Z= 0.307 Angle : 0.545 4.801 11262 Z= 0.289 Chirality : 0.041 0.361 1260 Planarity : 0.005 0.050 1451 Dihedral : 6.875 163.003 1157 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.25 % Allowed : 24.29 % Favored : 71.46 % 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: 1.06 (0.26), residues: 1039 helix: 2.07 (0.26), residues: 397 sheet: 0.09 (0.33), residues: 225 loop : -0.20 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.003 0.001 HIS R 220 PHE 0.013 0.002 PHE R 184 TYR 0.009 0.001 TYR B 59 ARG 0.004 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: B 256 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7752 (mtp85) REVERT: G 38 MET cc_start: 0.7949 (ttm) cc_final: 0.7630 (ttm) REVERT: R 6 ARG cc_start: 0.4686 (OUTLIER) cc_final: 0.3956 (mmt180) REVERT: R 72 PHE cc_start: 0.7803 (m-10) cc_final: 0.7319 (m-10) REVERT: R 215 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7293 (ttp-110) outliers start: 36 outliers final: 17 residues processed: 155 average time/residue: 2.7737 time to fit residues: 453.7443 Evaluate side-chains 133 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 254 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8318 Z= 0.376 Angle : 0.589 4.986 11262 Z= 0.314 Chirality : 0.043 0.361 1260 Planarity : 0.006 0.079 1451 Dihedral : 6.366 127.162 1157 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.83 % Allowed : 23.35 % Favored : 71.82 % 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: 1039 helix: 1.88 (0.26), residues: 397 sheet: -0.01 (0.33), residues: 225 loop : -0.25 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.002 PHE R 184 TYR 0.009 0.002 TYR A 329 ARG 0.010 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: B 256 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: R 6 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.4064 (mmt180) REVERT: R 19 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7417 (m) REVERT: R 215 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7303 (ttp-110) outliers start: 41 outliers final: 20 residues processed: 148 average time/residue: 2.9714 time to fit residues: 462.6524 Evaluate side-chains 136 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 ASP Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 380 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8318 Z= 0.236 Angle : 0.524 4.830 11262 Z= 0.276 Chirality : 0.041 0.358 1260 Planarity : 0.004 0.047 1451 Dihedral : 5.900 110.956 1157 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.07 % Allowed : 24.88 % Favored : 72.05 % 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: 1.20 (0.26), residues: 1039 helix: 2.19 (0.27), residues: 398 sheet: 0.31 (0.35), residues: 202 loop : -0.22 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.002 0.001 HIS R 220 PHE 0.016 0.001 PHE R 184 TYR 0.009 0.001 TYR A 329 ARG 0.007 0.000 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: B 256 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7729 (mtp85) REVERT: G 38 MET cc_start: 0.7955 (ttm) cc_final: 0.7628 (ttm) REVERT: G 62 ARG cc_start: 0.5037 (ptt-90) cc_final: 0.4833 (ptt-90) REVERT: R 6 ARG cc_start: 0.4736 (OUTLIER) cc_final: 0.4134 (mmt180) REVERT: R 215 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7300 (ttp-110) outliers start: 26 outliers final: 12 residues processed: 135 average time/residue: 3.1779 time to fit residues: 450.0703 Evaluate side-chains 122 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8318 Z= 0.231 Angle : 0.518 4.790 11262 Z= 0.273 Chirality : 0.040 0.359 1260 Planarity : 0.004 0.066 1451 Dihedral : 5.679 100.492 1157 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 25.12 % Favored : 72.29 % 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: 1.25 (0.27), residues: 1039 helix: 2.30 (0.26), residues: 397 sheet: 0.15 (0.34), residues: 218 loop : -0.15 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE R 184 TYR 0.008 0.001 TYR A 329 ARG 0.012 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: B 256 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7715 (mtp85) REVERT: G 38 MET cc_start: 0.7965 (ttm) cc_final: 0.7647 (ttm) REVERT: R 6 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.4132 (mmt180) REVERT: R 215 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7300 (ttp-110) outliers start: 22 outliers final: 12 residues processed: 132 average time/residue: 3.2063 time to fit residues: 445.0953 Evaluate side-chains 126 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 254 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8318 Z= 0.227 Angle : 0.519 5.673 11262 Z= 0.271 Chirality : 0.040 0.359 1260 Planarity : 0.004 0.068 1451 Dihedral : 5.544 92.331 1157 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.36 % Allowed : 25.35 % Favored : 72.29 % 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: 1.29 (0.27), residues: 1039 helix: 2.34 (0.27), residues: 398 sheet: 0.14 (0.34), residues: 218 loop : -0.14 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 211 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE R 184 TYR 0.008 0.001 TYR A 329 ARG 0.012 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: B 256 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7697 (mtp85) REVERT: G 38 MET cc_start: 0.7959 (ttm) cc_final: 0.7643 (ttm) REVERT: R 6 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.4134 (mmt180) REVERT: R 215 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7296 (ttp-110) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 3.1739 time to fit residues: 429.7568 Evaluate side-chains 125 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 ASP Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8318 Z= 0.268 Angle : 0.538 4.722 11262 Z= 0.284 Chirality : 0.041 0.359 1260 Planarity : 0.005 0.076 1451 Dihedral : 5.634 90.553 1157 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.59 % Allowed : 25.71 % Favored : 71.70 % 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: 1039 helix: 2.27 (0.27), residues: 398 sheet: 0.10 (0.34), residues: 218 loop : -0.17 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.003 0.001 HIS A 352 PHE 0.014 0.001 PHE R 184 TYR 0.009 0.001 TYR A 329 ARG 0.014 0.001 ARG R 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue VAL 100 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 61 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: B 256 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: G 38 MET cc_start: 0.7971 (ttm) cc_final: 0.7660 (ttm) REVERT: R 6 ARG cc_start: 0.4708 (OUTLIER) cc_final: 0.4219 (mmt180) REVERT: R 86 ARG cc_start: 0.4261 (mtm-85) cc_final: 0.3906 (mpp-170) REVERT: R 215 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7297 (ttp-110) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 3.2427 time to fit residues: 438.4490 Evaluate side-chains 130 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 ASP Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 254 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.076241 restraints weight = 40582.733| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.56 r_work: 0.2990 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8318 Z= 0.227 Angle : 0.523 5.330 11262 Z= 0.274 Chirality : 0.040 0.358 1260 Planarity : 0.004 0.074 1451 Dihedral : 5.441 80.989 1157 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.71 % Allowed : 25.59 % Favored : 71.70 % 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: 1.29 (0.27), residues: 1039 helix: 2.37 (0.27), residues: 399 sheet: 0.17 (0.34), residues: 216 loop : -0.18 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 290 HIS 0.002 0.001 HIS A 347 PHE 0.013 0.001 PHE R 184 TYR 0.008 0.001 TYR A 329 ARG 0.013 0.001 ARG R 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8287.89 seconds wall clock time: 142 minutes 50.11 seconds (8570.11 seconds total)