Starting phenix.real_space_refine on Fri Feb 16 14:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/02_2024/7jjo_22357_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/02_2024/7jjo_22357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/02_2024/7jjo_22357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/02_2024/7jjo_22357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/02_2024/7jjo_22357_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/02_2024/7jjo_22357_trim_updated.pdb" } resolution = 2.6 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= 1.248 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 51 5.16 5 C 5011 2.51 5 N 1379 2.21 5 O 1451 1.98 5 H 7749 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ARG 359": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "R ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 195": "OD1" <-> "OD2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 284": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15641 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3310 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 882 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 4434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4434 Unusual residues: {'5FW': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 268, None: 1} Not linked: pdbres="LEU R 357 " pdbres="5FW R 401 " Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 6.18, per 1000 atoms: 0.40 Number of scatterers: 15641 At special positions: 0 Unit cell: (81.396, 100.016, 138.852, 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 51 16.00 O 1451 8.00 N 1379 7.00 C 5011 6.00 H 7749 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.28 Conformation dependent library (CDL) restraints added in 1.4 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 38.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain '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 'A' and resid 16 through 37 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 299 through 302 removed outlier: 3.611A pdb=" N ALA A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.772A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 Processing helix chain 'G' and resid 9 through 21 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 41 through 68 Processing helix chain 'R' and resid 70 through 72 No H-bonds generated for 'chain 'R' and resid 70 through 72' Processing helix chain 'R' and resid 76 through 104 removed outlier: 4.726A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 111 through 144 Processing helix chain 'R' and resid 149 through 152 No H-bonds generated for 'chain 'R' and resid 149 through 152' Processing helix chain 'R' and resid 155 through 178 removed outlier: 4.576A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 187 through 194 Processing helix chain 'R' and resid 205 through 215 Processing helix chain 'R' and resid 217 through 241 Processing helix chain 'R' and resid 248 through 315 Proline residue: R 305 - end of helix Processing helix chain 'R' and resid 322 through 337 removed outlier: 4.030A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA R 337 " --> pdb=" O TYR R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 343 Processing helix chain 'R' and resid 347 through 356 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.128A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.812A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.972A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.799A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.517A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.534A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.027A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 345 through 349 removed outlier: 7.177A pdb=" N VAL A 273 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS A 348 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 275 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 234 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 229 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN A 204 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU A 43 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS A 206 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 45 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 208 " --> pdb=" O LEU A 45 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1080 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: 6.30 Time building geometry restraints manager: 13.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7723 1.03 - 1.23: 44 1.23 - 1.42: 3415 1.42 - 1.62: 4548 1.62 - 1.81: 70 Bond restraints: 15800 Sorted by residual: bond pdb=" N GLN N 1 " pdb=" H1 GLN N 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.437 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.416 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.491 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.548 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 15795 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.37: 447 107.37 - 114.03: 18385 114.03 - 120.69: 5551 120.69 - 127.35: 3930 127.35 - 134.02: 87 Bond angle restraints: 28400 Sorted by residual: angle pdb=" CA LYS G 14 " pdb=" CB LYS G 14 " pdb=" CG LYS G 14 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 angle pdb=" C ARG G 13 " pdb=" N LYS G 14 " pdb=" CA LYS G 14 " ideal model delta sigma weight residual 121.94 117.16 4.78 2.00e+00 2.50e-01 5.72e+00 angle pdb=" N GLY B 319 " pdb=" CA GLY B 319 " pdb=" C GLY B 319 " ideal model delta sigma weight residual 113.18 118.48 -5.30 2.37e+00 1.78e-01 5.00e+00 angle pdb=" CA GLN N 1 " pdb=" N GLN N 1 " pdb=" H1 GLN N 1 " ideal model delta sigma weight residual 120.00 113.57 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 108.99 5.53 3.00e+00 1.11e-01 3.39e+00 ... (remaining 28395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6814 17.86 - 35.72: 446 35.72 - 53.58: 136 53.58 - 71.44: 35 71.44 - 89.30: 12 Dihedral angle restraints: 7443 sinusoidal: 3974 harmonic: 3469 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -116.96 30.96 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA LYS G 14 " pdb=" C LYS G 14 " pdb=" N LEU G 15 " pdb=" CA LEU G 15 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1067 0.055 - 0.111: 136 0.111 - 0.166: 31 0.166 - 0.221: 0 0.221 - 0.277: 1 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.57 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LYS G 14 " pdb=" N LYS G 14 " pdb=" C LYS G 14 " pdb=" CB LYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1232 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 56 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C VAL R 56 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL R 56 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA R 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 14 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LYS G 14 " 0.026 2.00e-02 2.50e+03 pdb=" O LYS G 14 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU G 15 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 214 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C ARG A 214 " 0.021 2.00e-02 2.50e+03 pdb=" O ARG A 214 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP A 215 " -0.007 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 640 2.19 - 2.79: 31245 2.79 - 3.39: 42420 3.39 - 4.00: 56984 4.00 - 4.60: 87890 Nonbonded interactions: 219179 Sorted by model distance: nonbonded pdb=" HE1 TRP B 63 " pdb=" O GLY B 319 " model vdw 1.583 1.850 nonbonded pdb=" OE1 GLN N 53 " pdb=" H GLN N 53 " model vdw 1.672 1.850 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.678 1.850 nonbonded pdb=" OD1 ASP B 186 " pdb="HH11 ARG A 214 " model vdw 1.684 1.850 nonbonded pdb=" OD1 ASP B 66 " pdb=" H LEU B 69 " model vdw 1.687 1.850 ... (remaining 219174 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: 11.810 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: 0.230 Extract box with map and model: 29.270 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 50.950 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.084 8051 Z= 0.191 Angle : 0.478 5.526 10913 Z= 0.277 Chirality : 0.040 0.277 1235 Planarity : 0.003 0.026 1389 Dihedral : 14.278 89.304 2885 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.78 % Allowed : 12.44 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 980 helix: -0.05 (0.24), residues: 388 sheet: -0.27 (0.36), residues: 195 loop : -1.61 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 41 PHE 0.009 0.001 PHE R 225 TYR 0.008 0.001 TYR R 207 ARG 0.002 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.6969 (ptm) cc_final: 0.6608 (mmm) REVERT: B 219 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7607 (mmt90) REVERT: N 43 LYS cc_start: 0.8416 (mttt) cc_final: 0.8122 (mttm) REVERT: N 50 ASP cc_start: 0.8072 (p0) cc_final: 0.7848 (p0) REVERT: A 25 LYS cc_start: 0.7479 (tttt) cc_final: 0.7257 (ttmm) REVERT: A 34 LYS cc_start: 0.7548 (tttt) cc_final: 0.7347 (tttm) REVERT: A 194 PHE cc_start: 0.7336 (m-80) cc_final: 0.6988 (m-80) REVERT: A 199 GLN cc_start: 0.8805 (tt0) cc_final: 0.8533 (tt0) REVERT: A 260 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7780 (ttpp) REVERT: A 266 ARG cc_start: 0.7853 (ptm160) cc_final: 0.7573 (ptm160) REVERT: A 330 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 333 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7712 (ttp80) REVERT: G 38 MET cc_start: 0.7797 (ttp) cc_final: 0.7573 (ttm) REVERT: G 42 GLU cc_start: 0.7328 (tt0) cc_final: 0.7119 (tp30) REVERT: R 73 GLN cc_start: 0.8402 (mt0) cc_final: 0.8094 (mt0) REVERT: R 290 LYS cc_start: 0.7378 (ttpt) cc_final: 0.7001 (mtmt) outliers start: 15 outliers final: 9 residues processed: 246 average time/residue: 2.3913 time to fit residues: 624.9094 Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 176 GLN N 5 GLN G 24 ASN R 59 ASN ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8051 Z= 0.166 Angle : 0.449 5.259 10913 Z= 0.246 Chirality : 0.040 0.131 1235 Planarity : 0.003 0.047 1389 Dihedral : 5.506 59.406 1111 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.61 % Allowed : 17.42 % Favored : 79.98 % 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: -0.01 (0.26), residues: 980 helix: 1.09 (0.26), residues: 388 sheet: -0.04 (0.35), residues: 207 loop : -1.07 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 206 PHE 0.012 0.001 PHE R 225 TYR 0.009 0.001 TYR R 207 ARG 0.004 0.000 ARG R 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.6990 (ptm) cc_final: 0.6614 (mmm) REVERT: B 219 ARG cc_start: 0.7898 (mmt180) cc_final: 0.7658 (mmt90) REVERT: N 21 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8428 (m) REVERT: N 43 LYS cc_start: 0.8359 (mttt) cc_final: 0.8060 (mttm) REVERT: N 50 ASP cc_start: 0.8077 (p0) cc_final: 0.7837 (p0) REVERT: A 25 LYS cc_start: 0.7521 (tttt) cc_final: 0.7280 (ttmm) REVERT: A 34 LYS cc_start: 0.7574 (tttt) cc_final: 0.7369 (tttm) REVERT: A 194 PHE cc_start: 0.7354 (m-80) cc_final: 0.7006 (m-80) REVERT: A 199 GLN cc_start: 0.8784 (tt0) cc_final: 0.8518 (tt0) REVERT: A 260 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7798 (ttpp) REVERT: A 266 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7619 (ptm160) REVERT: A 330 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6854 (mm-30) REVERT: G 38 MET cc_start: 0.7813 (ttp) cc_final: 0.7589 (ttm) REVERT: R 73 GLN cc_start: 0.8413 (mt0) cc_final: 0.8117 (mt0) REVERT: R 290 LYS cc_start: 0.7368 (ttpt) cc_final: 0.6996 (mtmt) outliers start: 22 outliers final: 10 residues processed: 217 average time/residue: 2.4528 time to fit residues: 564.9331 Evaluate side-chains 210 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 119 ASN B 155 ASN B 176 GLN B 293 ASN N 5 GLN R 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8051 Z= 0.224 Angle : 0.474 6.104 10913 Z= 0.262 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.050 1389 Dihedral : 5.511 59.965 1106 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.44 % Allowed : 17.42 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 980 helix: 1.43 (0.27), residues: 390 sheet: 0.26 (0.35), residues: 207 loop : -0.77 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.001 PHE R 225 TYR 0.010 0.001 TYR R 207 ARG 0.007 0.000 ARG R 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8319 (m-30) cc_final: 0.8045 (m-30) REVERT: B 214 ARG cc_start: 0.7677 (mpt90) cc_final: 0.7415 (mmt180) REVERT: B 217 MET cc_start: 0.6996 (ptm) cc_final: 0.6628 (mmm) REVERT: B 219 ARG cc_start: 0.7947 (mmt180) cc_final: 0.7708 (mmt90) REVERT: N 21 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8425 (m) REVERT: N 43 LYS cc_start: 0.8348 (mttt) cc_final: 0.8047 (mttm) REVERT: N 50 ASP cc_start: 0.8124 (p0) cc_final: 0.7892 (p0) REVERT: A 25 LYS cc_start: 0.7560 (tttt) cc_final: 0.7298 (ttmm) REVERT: A 27 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 34 LYS cc_start: 0.7634 (tttt) cc_final: 0.7406 (tttm) REVERT: A 199 GLN cc_start: 0.8788 (tt0) cc_final: 0.8529 (tt0) REVERT: A 260 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7857 (ttpp) REVERT: A 266 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7700 (ptm160) REVERT: G 38 MET cc_start: 0.7854 (ttp) cc_final: 0.7625 (ttm) REVERT: R 73 GLN cc_start: 0.8439 (mt0) cc_final: 0.8153 (mt0) REVERT: R 232 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7437 (ttp-170) REVERT: R 290 LYS cc_start: 0.7378 (ttpt) cc_final: 0.7008 (mtmt) outliers start: 29 outliers final: 16 residues processed: 212 average time/residue: 2.4179 time to fit residues: 544.5720 Evaluate side-chains 215 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8051 Z= 0.243 Angle : 0.484 6.380 10913 Z= 0.268 Chirality : 0.041 0.130 1235 Planarity : 0.004 0.051 1389 Dihedral : 5.458 59.944 1104 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.55 % Allowed : 18.01 % Favored : 78.44 % 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: 0.67 (0.27), residues: 980 helix: 1.55 (0.27), residues: 392 sheet: 0.38 (0.35), residues: 207 loop : -0.64 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 206 PHE 0.014 0.001 PHE R 225 TYR 0.010 0.001 TYR R 207 ARG 0.009 0.000 ARG R 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6662 (mpt90) REVERT: B 96 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7371 (mtt180) REVERT: B 186 ASP cc_start: 0.8324 (m-30) cc_final: 0.8063 (m-30) REVERT: B 214 ARG cc_start: 0.7693 (mpt90) cc_final: 0.7437 (mmt180) REVERT: B 217 MET cc_start: 0.7017 (ptm) cc_final: 0.6633 (mmm) REVERT: B 219 ARG cc_start: 0.7956 (mmt180) cc_final: 0.7700 (mmt90) REVERT: N 21 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8427 (m) REVERT: N 43 LYS cc_start: 0.8313 (mttt) cc_final: 0.8015 (mttm) REVERT: A 25 LYS cc_start: 0.7579 (tttt) cc_final: 0.7336 (ttmm) REVERT: A 27 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 34 LYS cc_start: 0.7689 (tttt) cc_final: 0.7454 (tttm) REVERT: A 195 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6350 (mt-10) REVERT: A 199 GLN cc_start: 0.8776 (tt0) cc_final: 0.8513 (tt0) REVERT: A 260 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7840 (ttpp) REVERT: A 266 ARG cc_start: 0.7934 (ptm160) cc_final: 0.7636 (ptm160) REVERT: A 330 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7140 (mm-30) REVERT: G 38 MET cc_start: 0.7856 (ttp) cc_final: 0.7629 (ttm) REVERT: R 73 GLN cc_start: 0.8445 (mt0) cc_final: 0.8230 (mt0) REVERT: R 232 ARG cc_start: 0.7693 (ttm170) cc_final: 0.7448 (ttp-170) REVERT: R 290 LYS cc_start: 0.7392 (ttpt) cc_final: 0.7018 (mtmt) outliers start: 30 outliers final: 15 residues processed: 209 average time/residue: 2.5024 time to fit residues: 554.6645 Evaluate side-chains 208 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8051 Z= 0.260 Angle : 0.490 6.598 10913 Z= 0.272 Chirality : 0.041 0.131 1235 Planarity : 0.004 0.038 1389 Dihedral : 5.530 59.762 1104 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.32 % Allowed : 18.84 % Favored : 77.84 % 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: 0.78 (0.27), residues: 980 helix: 1.66 (0.27), residues: 392 sheet: 0.37 (0.34), residues: 212 loop : -0.57 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 41 PHE 0.014 0.001 PHE R 225 TYR 0.010 0.001 TYR R 207 ARG 0.004 0.000 ARG R 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8338 (m-30) cc_final: 0.8087 (m-30) REVERT: B 214 ARG cc_start: 0.7698 (mpt90) cc_final: 0.7435 (mmt180) REVERT: B 217 MET cc_start: 0.7028 (ptm) cc_final: 0.6642 (mmm) REVERT: B 219 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7714 (mmt90) REVERT: N 21 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8420 (m) REVERT: N 43 LYS cc_start: 0.8321 (mttt) cc_final: 0.8020 (mttm) REVERT: A 25 LYS cc_start: 0.7612 (tttt) cc_final: 0.7357 (ttmm) REVERT: A 27 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7662 (mm-30) REVERT: A 34 LYS cc_start: 0.7709 (tttt) cc_final: 0.7470 (tttm) REVERT: A 195 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6348 (mt-10) REVERT: A 199 GLN cc_start: 0.8777 (tt0) cc_final: 0.8521 (tt0) REVERT: A 260 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7824 (ttpp) REVERT: A 266 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7654 (ptm160) REVERT: A 330 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7226 (mm-30) REVERT: G 14 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5443 (pttt) REVERT: G 38 MET cc_start: 0.7851 (ttp) cc_final: 0.7629 (ttm) REVERT: R 73 GLN cc_start: 0.8450 (mt0) cc_final: 0.8243 (mt0) REVERT: R 232 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7447 (ttp-170) REVERT: R 290 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7017 (mtmt) outliers start: 28 outliers final: 15 residues processed: 208 average time/residue: 2.5633 time to fit residues: 564.6122 Evaluate side-chains 208 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN N 5 GLN R 150 GLN R 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8051 Z= 0.158 Angle : 0.452 6.031 10913 Z= 0.249 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.055 1389 Dihedral : 5.334 59.935 1104 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.96 % Allowed : 19.79 % Favored : 77.25 % 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: 1.02 (0.27), residues: 980 helix: 1.95 (0.27), residues: 390 sheet: 0.40 (0.34), residues: 207 loop : -0.45 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 206 PHE 0.012 0.001 PHE R 225 TYR 0.009 0.001 TYR N 115 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7393 (mmm-85) cc_final: 0.6634 (mpt90) REVERT: B 96 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7341 (mtt180) REVERT: B 186 ASP cc_start: 0.8268 (m-30) cc_final: 0.7985 (m-30) REVERT: B 214 ARG cc_start: 0.7689 (mpt90) cc_final: 0.7430 (mmt180) REVERT: B 217 MET cc_start: 0.7031 (ptm) cc_final: 0.6656 (mmm) REVERT: B 219 ARG cc_start: 0.7950 (mmt180) cc_final: 0.7706 (mmt90) REVERT: B 314 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8149 (ttm-80) REVERT: N 43 LYS cc_start: 0.8284 (mttt) cc_final: 0.7978 (mttm) REVERT: N 50 ASP cc_start: 0.8102 (p0) cc_final: 0.7885 (p0) REVERT: A 25 LYS cc_start: 0.7567 (tttt) cc_final: 0.7328 (ttmm) REVERT: A 27 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 34 LYS cc_start: 0.7654 (tttt) cc_final: 0.7421 (tttm) REVERT: A 195 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: A 199 GLN cc_start: 0.8766 (tt0) cc_final: 0.8512 (tt0) REVERT: A 260 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7792 (ttpp) REVERT: A 266 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7641 (ptm160) REVERT: G 14 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5547 (pttt) REVERT: G 38 MET cc_start: 0.7834 (ttp) cc_final: 0.7629 (ttm) REVERT: R 73 GLN cc_start: 0.8436 (mt0) cc_final: 0.8228 (mt0) REVERT: R 232 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7434 (ttp-170) REVERT: R 290 LYS cc_start: 0.7389 (ttpt) cc_final: 0.7001 (mtmt) outliers start: 25 outliers final: 12 residues processed: 205 average time/residue: 2.5793 time to fit residues: 564.9648 Evaluate side-chains 205 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN N 1 GLN N 5 GLN ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8051 Z= 0.177 Angle : 0.457 5.780 10913 Z= 0.252 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.044 1389 Dihedral : 5.360 59.968 1104 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.96 % Allowed : 20.26 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 980 helix: 2.06 (0.27), residues: 392 sheet: 0.46 (0.34), residues: 207 loop : -0.44 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 206 PHE 0.012 0.001 PHE R 225 TYR 0.009 0.001 TYR R 207 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7367 (mtt180) REVERT: B 175 GLN cc_start: 0.7826 (mm110) cc_final: 0.7576 (mm110) REVERT: B 186 ASP cc_start: 0.8286 (m-30) cc_final: 0.8010 (m-30) REVERT: B 214 ARG cc_start: 0.7693 (mpt90) cc_final: 0.7345 (mmt180) REVERT: B 217 MET cc_start: 0.7024 (ptm) cc_final: 0.6659 (mmm) REVERT: B 219 ARG cc_start: 0.7961 (mmt180) cc_final: 0.7714 (mmt90) REVERT: B 314 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8156 (ttm-80) REVERT: N 21 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8414 (m) REVERT: N 43 LYS cc_start: 0.8247 (mttt) cc_final: 0.7940 (mttm) REVERT: N 50 ASP cc_start: 0.8126 (p0) cc_final: 0.7903 (p0) REVERT: A 25 LYS cc_start: 0.7573 (tttt) cc_final: 0.7331 (ttmm) REVERT: A 27 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 34 LYS cc_start: 0.7662 (tttt) cc_final: 0.7424 (tttm) REVERT: A 199 GLN cc_start: 0.8771 (tt0) cc_final: 0.8519 (tt0) REVERT: A 260 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7787 (ttpp) REVERT: A 266 ARG cc_start: 0.7915 (ptm160) cc_final: 0.7665 (ptm160) REVERT: G 14 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5673 (pttt) REVERT: G 38 MET cc_start: 0.7816 (ttp) cc_final: 0.7598 (ttm) REVERT: R 232 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7439 (ttp-170) REVERT: R 290 LYS cc_start: 0.7380 (ttpt) cc_final: 0.6992 (mtmt) outliers start: 25 outliers final: 14 residues processed: 207 average time/residue: 2.4195 time to fit residues: 532.2628 Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8051 Z= 0.343 Angle : 0.526 7.075 10913 Z= 0.293 Chirality : 0.042 0.137 1235 Planarity : 0.004 0.063 1389 Dihedral : 5.690 59.619 1104 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.20 % Allowed : 20.62 % Favored : 76.18 % 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: 980 helix: 1.86 (0.26), residues: 391 sheet: 0.51 (0.35), residues: 205 loop : -0.47 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 220 HIS 0.004 0.001 HIS A 206 PHE 0.016 0.002 PHE R 225 TYR 0.011 0.001 TYR N 115 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7843 (mm110) cc_final: 0.7570 (mm110) REVERT: B 186 ASP cc_start: 0.8390 (m-30) cc_final: 0.8180 (m-30) REVERT: B 214 ARG cc_start: 0.7630 (mpt90) cc_final: 0.7385 (mmt180) REVERT: B 217 MET cc_start: 0.7021 (ptm) cc_final: 0.6657 (mmm) REVERT: B 219 ARG cc_start: 0.7982 (mmt180) cc_final: 0.7613 (mmt90) REVERT: N 43 LYS cc_start: 0.8320 (mttt) cc_final: 0.8013 (mttm) REVERT: A 25 LYS cc_start: 0.7662 (tttt) cc_final: 0.7380 (ttmm) REVERT: A 27 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 34 LYS cc_start: 0.7721 (tttt) cc_final: 0.7459 (tttm) REVERT: A 199 GLN cc_start: 0.8777 (tt0) cc_final: 0.8535 (tt0) REVERT: A 260 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7834 (ttpp) REVERT: A 266 ARG cc_start: 0.7954 (ptm160) cc_final: 0.7704 (ptm160) REVERT: G 14 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5827 (pttt) REVERT: R 232 ARG cc_start: 0.7706 (ttm170) cc_final: 0.7458 (ttp-170) REVERT: R 290 LYS cc_start: 0.7428 (ttpt) cc_final: 0.7032 (mtmt) REVERT: R 301 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8382 (tm) outliers start: 27 outliers final: 17 residues processed: 207 average time/residue: 2.5473 time to fit residues: 558.2380 Evaluate side-chains 204 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 83 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 77 ASN R 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8051 Z= 0.163 Angle : 0.460 6.214 10913 Z= 0.254 Chirality : 0.040 0.133 1235 Planarity : 0.004 0.061 1389 Dihedral : 5.439 59.791 1104 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.49 % Allowed : 21.21 % Favored : 76.30 % 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: 980 helix: 2.17 (0.27), residues: 388 sheet: 0.56 (0.35), residues: 205 loop : -0.36 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 206 PHE 0.013 0.001 PHE R 225 TYR 0.009 0.001 TYR R 207 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7836 (mm110) cc_final: 0.7569 (mm110) REVERT: B 186 ASP cc_start: 0.8285 (m-30) cc_final: 0.8001 (m-30) REVERT: B 214 ARG cc_start: 0.7629 (mpt90) cc_final: 0.7367 (mmt180) REVERT: B 217 MET cc_start: 0.7026 (ptm) cc_final: 0.6670 (mmm) REVERT: B 219 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7723 (mmt90) REVERT: B 314 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8175 (ttm-80) REVERT: N 43 LYS cc_start: 0.8277 (mttt) cc_final: 0.7967 (mttm) REVERT: N 50 ASP cc_start: 0.8093 (p0) cc_final: 0.7881 (p0) REVERT: A 25 LYS cc_start: 0.7589 (tttt) cc_final: 0.7330 (ttmm) REVERT: A 27 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 34 LYS cc_start: 0.7670 (tttt) cc_final: 0.7427 (tttm) REVERT: A 199 GLN cc_start: 0.8770 (tt0) cc_final: 0.8523 (tt0) REVERT: A 260 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7778 (ttpp) REVERT: A 266 ARG cc_start: 0.7917 (ptm160) cc_final: 0.7670 (ptm160) REVERT: G 14 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.6058 (pttt) REVERT: R 232 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7443 (ttp-170) REVERT: R 290 LYS cc_start: 0.7384 (ttpt) cc_final: 0.6993 (mtmt) outliers start: 21 outliers final: 15 residues processed: 206 average time/residue: 2.5745 time to fit residues: 561.3842 Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN N 5 GLN R 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8051 Z= 0.176 Angle : 0.458 5.743 10913 Z= 0.253 Chirality : 0.040 0.130 1235 Planarity : 0.004 0.064 1389 Dihedral : 5.372 59.560 1104 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.13 % Allowed : 21.68 % Favored : 76.18 % 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: 1.36 (0.27), residues: 980 helix: 2.31 (0.27), residues: 388 sheet: 0.55 (0.34), residues: 210 loop : -0.33 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 206 PHE 0.012 0.001 PHE A 198 TYR 0.010 0.001 TYR R 207 ARG 0.010 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LEU 357 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7834 (mm110) cc_final: 0.7556 (mm110) REVERT: B 186 ASP cc_start: 0.8293 (m-30) cc_final: 0.8022 (m-30) REVERT: B 214 ARG cc_start: 0.7614 (mpt90) cc_final: 0.7363 (mmt180) REVERT: B 217 MET cc_start: 0.7017 (ptm) cc_final: 0.6673 (mmm) REVERT: B 219 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7730 (mmt90) REVERT: N 43 LYS cc_start: 0.8244 (mttt) cc_final: 0.7934 (mttm) REVERT: N 50 ASP cc_start: 0.8119 (p0) cc_final: 0.7898 (p0) REVERT: A 25 LYS cc_start: 0.7593 (tttt) cc_final: 0.7338 (ttmm) REVERT: A 27 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 34 LYS cc_start: 0.7666 (tttt) cc_final: 0.7423 (tttm) REVERT: A 199 GLN cc_start: 0.8766 (tt0) cc_final: 0.8516 (tt0) REVERT: A 260 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7783 (ttpp) REVERT: A 266 ARG cc_start: 0.7920 (ptm160) cc_final: 0.7682 (ptm160) REVERT: R 232 ARG cc_start: 0.7693 (ttm170) cc_final: 0.7441 (ttp-170) REVERT: R 290 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6975 (mtmt) outliers start: 18 outliers final: 15 residues processed: 200 average time/residue: 2.4922 time to fit residues: 528.5287 Evaluate side-chains 206 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN N 5 GLN R 77 ASN R 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114817 restraints weight = 24755.206| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.83 r_work: 0.3129 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8051 Z= 0.203 Angle : 0.472 6.120 10913 Z= 0.260 Chirality : 0.040 0.130 1235 Planarity : 0.004 0.064 1389 Dihedral : 5.416 59.347 1104 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.01 % Allowed : 22.51 % Favored : 75.47 % 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: 1.37 (0.27), residues: 980 helix: 2.30 (0.27), residues: 388 sheet: 0.56 (0.34), residues: 210 loop : -0.31 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 206 PHE 0.012 0.001 PHE R 225 TYR 0.010 0.001 TYR R 207 ARG 0.008 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9252.21 seconds wall clock time: 162 minutes 41.41 seconds (9761.41 seconds total)