Starting phenix.real_space_refine on Thu Nov 16 14:04:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/11_2023/7jjo_22357_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/11_2023/7jjo_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_22357/11_2023/7jjo_22357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/11_2023/7jjo_22357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/11_2023/7jjo_22357_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjo_22357/11_2023/7jjo_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 7.16, per 1000 atoms: 0.46 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: 12.15 Conformation dependent library (CDL) restraints added in 1.5 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: 2.81 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: 5.35 Time building geometry restraints manager: 12.39 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: 5903 17.86 - 35.72: 377 35.72 - 53.58: 85 53.58 - 71.44: 21 71.44 - 89.30: 12 Dihedral angle restraints: 6398 sinusoidal: 2929 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 6395 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.710 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: 0.250 Extract box with map and model: 27.550 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 50.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.850 ------------------------------------------------------------------------------- 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 : 14.210 89.304 2879 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 *********************** 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 : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 246 average time/residue: 2.3925 time to fit residues: 625.7863 Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1685 time to fit residues: 2.4031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 A 199 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1598 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= 0.177 Angle : 0.463 5.236 10913 Z= 0.252 Chirality : 0.040 0.132 1235 Planarity : 0.004 0.044 1389 Dihedral : 4.180 23.902 1093 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.20 % Allowed : 17.77 % Favored : 79.03 % 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: -0.00 (0.26), residues: 980 helix: 1.07 (0.26), residues: 388 sheet: -0.01 (0.35), residues: 207 loop : -1.06 (0.30), residues: 385 *********************** 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 229 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 219 average time/residue: 2.4049 time to fit residues: 564.3344 Evaluate side-chains 211 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.2775 time to fit residues: 2.9329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 176 GLN B 293 ASN N 5 GLN A 199 GLN ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1818 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= 0.182 Angle : 0.462 5.619 10913 Z= 0.253 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.052 1389 Dihedral : 4.205 21.195 1093 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.67 % Allowed : 18.13 % Favored : 78.20 % 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: 0.56 (0.27), residues: 980 helix: 1.52 (0.27), residues: 390 sheet: 0.25 (0.35), residues: 207 loop : -0.72 (0.31), residues: 383 *********************** 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 227 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 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 outliers start: 31 outliers final: 18 residues processed: 215 average time/residue: 2.4594 time to fit residues: 562.0212 Evaluate side-chains 212 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 6 average time/residue: 0.4215 time to fit residues: 4.9313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 A 199 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: 0.8111 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8051 Z= 0.177 Angle : 0.461 5.542 10913 Z= 0.251 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.047 1389 Dihedral : 4.192 20.017 1093 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.67 % Allowed : 18.60 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 980 helix: 1.73 (0.27), residues: 391 sheet: 0.34 (0.34), residues: 207 loop : -0.61 (0.32), residues: 382 *********************** 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 228 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 215 average time/residue: 2.4689 time to fit residues: 564.2188 Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.4835 time to fit residues: 5.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN A 199 GLN R 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2273 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= 0.349 Angle : 0.539 7.030 10913 Z= 0.299 Chirality : 0.042 0.138 1235 Planarity : 0.004 0.060 1389 Dihedral : 4.612 21.698 1093 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.91 % Allowed : 19.19 % Favored : 76.90 % 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: 0.74 (0.27), residues: 980 helix: 1.62 (0.26), residues: 391 sheet: 0.43 (0.35), residues: 206 loop : -0.60 (0.31), residues: 383 *********************** 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 227 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 212 average time/residue: 2.5702 time to fit residues: 576.9915 Evaluate side-chains 204 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.4819 time to fit residues: 5.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 23 optimal weight: 0.5980 chunk 94 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN A 357 ASN R 77 ASN R 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2318 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= 0.190 Angle : 0.485 6.448 10913 Z= 0.266 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.052 1389 Dihedral : 4.432 20.983 1093 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.08 % Allowed : 20.97 % Favored : 75.95 % 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: 1.01 (0.27), residues: 980 helix: 1.91 (0.27), residues: 388 sheet: 0.44 (0.34), residues: 207 loop : -0.45 (0.32), residues: 385 *********************** 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 221 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 211 average time/residue: 2.5004 time to fit residues: 559.4869 Evaluate side-chains 209 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.2137 time to fit residues: 3.2755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 94 optimal weight: 0.0470 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- 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 A 199 GLN R 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8051 Z= 0.158 Angle : 0.464 5.748 10913 Z= 0.253 Chirality : 0.040 0.132 1235 Planarity : 0.003 0.049 1389 Dihedral : 4.240 19.628 1093 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.96 % Allowed : 21.33 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 980 helix: 2.17 (0.27), residues: 388 sheet: 0.50 (0.34), residues: 207 loop : -0.39 (0.32), residues: 385 *********************** 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 223 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 214 average time/residue: 2.4386 time to fit residues: 555.1665 Evaluate side-chains 208 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.6750 time to fit residues: 4.9577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 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: 0.6980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 A 199 GLN R 77 ASN R 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8051 Z= 0.249 Angle : 0.499 6.228 10913 Z= 0.274 Chirality : 0.041 0.130 1235 Planarity : 0.004 0.066 1389 Dihedral : 4.398 20.510 1093 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.49 % Allowed : 22.27 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 980 helix: 2.10 (0.27), residues: 388 sheet: 0.51 (0.34), residues: 210 loop : -0.38 (0.32), residues: 382 *********************** 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 213 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 206 average time/residue: 2.4503 time to fit residues: 536.9011 Evaluate side-chains 203 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2079 time to fit residues: 2.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.4980 chunk 88 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 83 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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 A 199 GLN R 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8051 Z= 0.121 Angle : 0.451 5.495 10913 Z= 0.244 Chirality : 0.039 0.134 1235 Planarity : 0.003 0.048 1389 Dihedral : 4.140 19.083 1093 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.90 % Allowed : 22.51 % Favored : 75.59 % 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: 1.39 (0.27), residues: 980 helix: 2.37 (0.27), residues: 388 sheet: 0.48 (0.33), residues: 212 loop : -0.31 (0.33), residues: 380 *********************** 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: 16 poor density : 198 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 212 average time/residue: 2.4518 time to fit residues: 551.7935 Evaluate side-chains 210 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.3182 time to fit residues: 2.0335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 A 199 GLN R 77 ASN R 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2465 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= 0.210 Angle : 0.485 6.541 10913 Z= 0.264 Chirality : 0.040 0.129 1235 Planarity : 0.003 0.051 1389 Dihedral : 4.263 20.092 1093 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.78 % Allowed : 22.99 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 980 helix: 2.34 (0.27), residues: 388 sheet: 0.60 (0.34), residues: 209 loop : -0.32 (0.32), residues: 383 ********************** 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 206 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 204 average time/residue: 2.5665 time to fit residues: 556.6197 Evaluate side-chains 203 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.2459 time to fit residues: 2.0053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 A 199 GLN R 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113704 restraints weight = 25103.443| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.79 r_work: 0.3150 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2513 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= 0.177 Angle : 0.473 5.899 10913 Z= 0.257 Chirality : 0.040 0.131 1235 Planarity : 0.004 0.070 1389 Dihedral : 4.248 19.941 1093 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.90 % Allowed : 22.75 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 980 helix: 2.40 (0.27), residues: 388 sheet: 0.60 (0.34), residues: 211 loop : -0.32 (0.32), residues: 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9351.05 seconds wall clock time: 164 minutes 39.02 seconds (9879.02 seconds total)