Starting phenix.real_space_refine on Wed Feb 14 05:44:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew1_31344/02_2024/7ew1_31344_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.004 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 61 5.16 5 C 5550 2.51 5 N 1492 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8735 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "D" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1832 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2035 Unusual residues: {'J8C': 1} Classifications: {'peptide': 269, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 255, None: 1} Not linked: pdbres="ASN A 310 " pdbres="J8C A 401 " Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7954 SG CYS A 197 54.361 65.194 28.586 1.00145.71 S Time building chain proxies: 4.98, per 1000 atoms: 0.57 Number of scatterers: 8735 At special positions: 0 Unit cell: (92.65, 124.95, 124.95, 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 61 16.00 F 3 9.00 O 1629 8.00 N 1492 7.00 C 5550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 182 " distance=1.48 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 282 " 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: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 16 sheets defined 30.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.585A pdb=" N SER D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 212 through 215 removed outlier: 3.581A pdb=" N PHE D 215 " --> pdb=" O ILE D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 242 through 254 removed outlier: 3.660A pdb=" N SER D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 280 Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.667A pdb=" N ALA D 300 " --> pdb=" O TYR D 296 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 351 removed outlier: 3.934A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 22 removed outlier: 3.588A pdb=" N TYR A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 removed outlier: 4.715A pdb=" N VAL A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N CYS A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 95 Processing helix chain 'A' and resid 105 through 138 removed outlier: 3.583A pdb=" N GLY A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.702A pdb=" N LEU A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 191 through 222 removed outlier: 4.317A pdb=" N LEU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.781A pdb=" N VAL A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 289 through 305 removed outlier: 3.963A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.900A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.555A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.654A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.739A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.363A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.709A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.714A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 220 through 224 removed outlier: 4.210A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS D 224 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 264 through 268 Processing sheet with id= K, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.475A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 115 through 117 removed outlier: 6.060A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.810A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= P, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.536A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 963 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: 2.39 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2834 1.34 - 1.46: 1948 1.46 - 1.58: 4035 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 8903 Sorted by residual: bond pdb=" C16 J8C A 401 " pdb=" C19 J8C A 401 " ideal model delta sigma weight residual 0.000 1.539 -1.539 2.00e-02 2.50e+03 5.92e+03 bond pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " ideal model delta sigma weight residual 1.958 1.534 0.424 2.00e-02 2.50e+03 4.49e+02 bond pdb=" C25 J8C A 401 " pdb=" F28 J8C A 401 " ideal model delta sigma weight residual 1.506 1.363 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C16 J8C A 401 " pdb=" C17 J8C A 401 " ideal model delta sigma weight residual 1.524 1.386 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C13 J8C A 401 " pdb=" C18 J8C A 401 " ideal model delta sigma weight residual 1.506 1.385 0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 8898 not shown) Histogram of bond angle deviations from ideal: 88.66 - 97.72: 4 97.72 - 106.79: 198 106.79 - 115.85: 5612 115.85 - 124.92: 6115 124.92 - 133.98: 135 Bond angle restraints: 12064 Sorted by residual: angle pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " pdb=" C14 J8C A 401 " ideal model delta sigma weight residual 105.15 120.49 -15.34 3.00e+00 1.11e-01 2.61e+01 angle pdb=" N VAL A 145 " pdb=" CA VAL A 145 " pdb=" C VAL A 145 " ideal model delta sigma weight residual 107.28 114.98 -7.70 1.59e+00 3.96e-01 2.35e+01 angle pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " pdb=" C18 J8C A 401 " ideal model delta sigma weight residual 133.75 119.57 14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N LEU A 135 " pdb=" CA LEU A 135 " pdb=" C LEU A 135 " ideal model delta sigma weight residual 111.28 116.24 -4.96 1.09e+00 8.42e-01 2.07e+01 angle pdb=" O GLY A 265 " pdb=" C GLY A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 121.07 122.57 -1.50 3.60e-01 7.72e+00 1.73e+01 ... (remaining 12059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 4945 21.46 - 42.93: 322 42.93 - 64.39: 28 64.39 - 85.85: 4 85.85 - 107.32: 6 Dihedral angle restraints: 5305 sinusoidal: 2049 harmonic: 3256 Sorted by residual: dihedral pdb=" C VAL A 185 " pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" CB VAL A 185 " ideal model delta harmonic sigma weight residual -122.00 -141.09 19.09 0 2.50e+00 1.60e-01 5.83e+01 dihedral pdb=" N VAL A 185 " pdb=" C VAL A 185 " pdb=" CA VAL A 185 " pdb=" CB VAL A 185 " ideal model delta harmonic sigma weight residual 123.40 140.52 -17.12 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" C19 J8C A 401 " pdb=" C20 J8C A 401 " pdb=" C21 J8C A 401 " pdb=" C22 J8C A 401 " ideal model delta sinusoidal sigma weight residual -53.20 54.12 -107.32 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1373 0.122 - 0.244: 11 0.244 - 0.366: 2 0.366 - 0.488: 0 0.488 - 0.610: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA VAL A 185 " pdb=" N VAL A 185 " pdb=" C VAL A 185 " pdb=" CB VAL A 185 " both_signs ideal model delta sigma weight residual False 2.44 1.83 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" CA ALA A 143 " pdb=" N ALA A 143 " pdb=" C ALA A 143 " pdb=" CB ALA A 143 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA THR A 136 " pdb=" N THR A 136 " pdb=" C THR A 136 " pdb=" CB THR A 136 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1384 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO E 75 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 97 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 98 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 104 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO A 105 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.016 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 17 2.26 - 2.92: 3594 2.92 - 3.58: 11887 3.58 - 4.24: 18668 4.24 - 4.90: 32178 Nonbonded interactions: 66344 Sorted by model distance: nonbonded pdb=" CD1 LEU A 17 " pdb=" CB LEU A 179 " model vdw 1.601 3.860 nonbonded pdb=" NE1 TRP A 264 " pdb=" ND2 ASN A 298 " model vdw 1.621 3.200 nonbonded pdb=" CE1 HIS A 18 " pdb=" SG CYS A 182 " model vdw 1.679 3.620 nonbonded pdb=" OG SER A 183 " pdb=" C ALA A 190 " model vdw 1.686 3.270 nonbonded pdb=" O HIS A 68 " pdb=" NH2 ARG A 148 " model vdw 1.783 2.520 ... (remaining 66339 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.140 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.200 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.018 1.539 8903 Z= 0.880 Angle : 0.677 15.336 12064 Z= 0.403 Chirality : 0.046 0.610 1387 Planarity : 0.003 0.046 1524 Dihedral : 13.908 107.318 3196 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 0.32 % Allowed : 5.97 % Favored : 93.71 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.94 % 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: -2.10 (0.24), residues: 1109 helix: 0.38 (0.29), residues: 341 sheet: -1.74 (0.28), residues: 279 loop : -2.47 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE E 80 TYR 0.006 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8235 (ptpp) REVERT: D 209 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8779 (ttpp) REVERT: D 242 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7943 (mtp85) REVERT: D 272 ASP cc_start: 0.7805 (p0) cc_final: 0.7133 (p0) REVERT: E 73 ASP cc_start: 0.7971 (t70) cc_final: 0.7682 (t70) REVERT: E 219 LEU cc_start: 0.7996 (tt) cc_final: 0.7761 (tt) REVERT: A 131 LEU cc_start: 0.7589 (tp) cc_final: 0.7370 (tp) outliers start: 3 outliers final: 0 residues processed: 161 average time/residue: 0.2538 time to fit residues: 55.2299 Evaluate side-chains 126 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 237 ASN B 239 ASN B 340 ASN C 24 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN E 82 GLN E 113 GLN E 194 ASN A 18 HIS ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 8903 Z= 0.422 Angle : 0.719 14.500 12064 Z= 0.353 Chirality : 0.045 0.232 1387 Planarity : 0.005 0.060 1524 Dihedral : 6.350 94.195 1233 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.35 % Allowed : 14.93 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.76 (0.24), residues: 1109 helix: 0.76 (0.29), residues: 353 sheet: -1.55 (0.28), residues: 286 loop : -2.43 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.007 0.002 HIS B 311 PHE 0.019 0.002 PHE A 72 TYR 0.030 0.002 TYR B 59 ARG 0.007 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8209 (ptpp) REVERT: D 242 ARG cc_start: 0.8278 (mtp85) cc_final: 0.8014 (mtp85) REVERT: E 73 ASP cc_start: 0.8044 (t70) cc_final: 0.7796 (t0) REVERT: E 109 ASP cc_start: 0.7974 (p0) cc_final: 0.7761 (p0) REVERT: E 183 GLN cc_start: 0.8031 (pm20) cc_final: 0.7798 (pm20) REVERT: A 131 LEU cc_start: 0.7603 (tp) cc_final: 0.7342 (tp) REVERT: A 193 TYR cc_start: 0.7627 (t80) cc_final: 0.7282 (t80) REVERT: A 292 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7138 (tt) outliers start: 22 outliers final: 17 residues processed: 145 average time/residue: 0.2396 time to fit residues: 46.4377 Evaluate side-chains 139 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.0070 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 0.0980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 268 ASN B 340 ASN D 52 GLN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN A 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 8903 Z= 0.183 Angle : 0.592 13.807 12064 Z= 0.286 Chirality : 0.040 0.194 1387 Planarity : 0.004 0.059 1524 Dihedral : 5.805 73.091 1233 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 2.35 % Allowed : 17.80 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1109 helix: 1.06 (0.29), residues: 352 sheet: -1.30 (0.29), residues: 285 loop : -2.22 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.003 0.001 HIS B 183 PHE 0.009 0.001 PHE A 72 TYR 0.015 0.001 TYR D 230 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8208 (ptpp) REVERT: E 73 ASP cc_start: 0.8016 (t70) cc_final: 0.7766 (t0) REVERT: A 131 LEU cc_start: 0.7609 (tp) cc_final: 0.7294 (tp) REVERT: A 193 TYR cc_start: 0.7627 (t80) cc_final: 0.7339 (t80) REVERT: A 216 TYR cc_start: 0.8048 (t80) cc_final: 0.7771 (t80) REVERT: A 292 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7117 (tt) outliers start: 22 outliers final: 14 residues processed: 141 average time/residue: 0.2174 time to fit residues: 42.3746 Evaluate side-chains 136 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8903 Z= 0.165 Angle : 0.562 11.121 12064 Z= 0.270 Chirality : 0.040 0.146 1387 Planarity : 0.003 0.053 1524 Dihedral : 5.538 64.188 1233 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.45 % Allowed : 18.66 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.16 (0.25), residues: 1109 helix: 1.18 (0.30), residues: 352 sheet: -1.13 (0.29), residues: 285 loop : -2.05 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 PHE 0.008 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.010 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.006 Fit side-chains REVERT: B 15 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8209 (ptpp) REVERT: B 291 ASP cc_start: 0.7420 (t0) cc_final: 0.7043 (t0) REVERT: B 338 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8203 (mm) REVERT: D 242 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8057 (mtp85) REVERT: E 73 ASP cc_start: 0.7991 (t70) cc_final: 0.7772 (t0) REVERT: A 131 LEU cc_start: 0.7671 (tp) cc_final: 0.7340 (tp) REVERT: A 193 TYR cc_start: 0.7647 (t80) cc_final: 0.7396 (t80) REVERT: A 216 TYR cc_start: 0.8014 (t80) cc_final: 0.7811 (t80) REVERT: A 292 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7099 (tt) outliers start: 23 outliers final: 15 residues processed: 146 average time/residue: 0.2100 time to fit residues: 42.0477 Evaluate side-chains 140 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8903 Z= 0.174 Angle : 0.558 11.007 12064 Z= 0.268 Chirality : 0.040 0.127 1387 Planarity : 0.003 0.053 1524 Dihedral : 5.403 62.538 1233 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 18.98 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1109 helix: 1.30 (0.30), residues: 352 sheet: -1.09 (0.29), residues: 287 loop : -1.93 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE B 199 TYR 0.017 0.001 TYR D 230 ARG 0.003 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8604 (ptpp) cc_final: 0.8212 (ptpp) REVERT: B 291 ASP cc_start: 0.7508 (t0) cc_final: 0.7184 (t0) REVERT: B 338 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8200 (mm) REVERT: D 242 ARG cc_start: 0.8454 (mtt180) cc_final: 0.8031 (mtp85) REVERT: E 43 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7665 (mmtm) REVERT: E 73 ASP cc_start: 0.7998 (t70) cc_final: 0.7787 (t0) REVERT: E 87 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7270 (mtt-85) REVERT: A 71 MET cc_start: 0.4219 (ttp) cc_final: 0.3650 (mmm) REVERT: A 131 LEU cc_start: 0.7717 (tp) cc_final: 0.7380 (tp) REVERT: A 193 TYR cc_start: 0.7639 (t80) cc_final: 0.7410 (t80) REVERT: A 292 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7132 (tt) outliers start: 28 outliers final: 21 residues processed: 143 average time/residue: 0.2196 time to fit residues: 43.0903 Evaluate side-chains 149 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 89 optimal weight: 0.0050 chunk 50 optimal weight: 0.0570 chunk 9 optimal weight: 0.0470 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 8903 Z= 0.132 Angle : 0.529 10.755 12064 Z= 0.252 Chirality : 0.039 0.131 1387 Planarity : 0.003 0.053 1524 Dihedral : 5.140 64.335 1233 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 1.71 % Allowed : 20.58 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.26), residues: 1109 helix: 1.46 (0.30), residues: 352 sheet: -0.88 (0.30), residues: 285 loop : -1.76 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.002 0.000 HIS B 183 PHE 0.009 0.001 PHE D 189 TYR 0.015 0.001 TYR A 216 ARG 0.005 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.233 Fit side-chains REVERT: B 15 LYS cc_start: 0.8603 (ptpp) cc_final: 0.8273 (ptpp) REVERT: B 291 ASP cc_start: 0.7521 (t0) cc_final: 0.7176 (t0) REVERT: D 242 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8034 (mtp85) REVERT: E 43 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7807 (mmtm) REVERT: E 87 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7261 (mtt-85) REVERT: E 223 ASP cc_start: 0.7641 (p0) cc_final: 0.7363 (p0) REVERT: A 71 MET cc_start: 0.3991 (ttp) cc_final: 0.3320 (mmm) REVERT: A 131 LEU cc_start: 0.7716 (tp) cc_final: 0.7378 (tp) outliers start: 16 outliers final: 14 residues processed: 143 average time/residue: 0.2238 time to fit residues: 43.5630 Evaluate side-chains 143 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8903 Z= 0.195 Angle : 0.566 10.884 12064 Z= 0.267 Chirality : 0.041 0.393 1387 Planarity : 0.003 0.053 1524 Dihedral : 5.112 65.628 1233 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.45 % Allowed : 19.83 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.72 (0.26), residues: 1109 helix: 1.47 (0.30), residues: 352 sheet: -0.86 (0.30), residues: 287 loop : -1.74 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 264 HIS 0.003 0.001 HIS E 232 PHE 0.013 0.001 PHE A 116 TYR 0.026 0.001 TYR A 193 ARG 0.003 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.880 Fit side-chains REVERT: B 15 LYS cc_start: 0.8609 (ptpp) cc_final: 0.8240 (ptpp) REVERT: B 291 ASP cc_start: 0.7560 (t0) cc_final: 0.7232 (t0) REVERT: D 242 ARG cc_start: 0.8429 (mtt180) cc_final: 0.7998 (mtp85) REVERT: E 43 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7849 (mmtm) REVERT: E 87 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7246 (mtt-85) REVERT: A 71 MET cc_start: 0.4020 (ttp) cc_final: 0.3344 (mmm) REVERT: A 131 LEU cc_start: 0.7706 (tp) cc_final: 0.7375 (tp) REVERT: A 261 VAL cc_start: 0.8470 (t) cc_final: 0.8122 (m) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.2135 time to fit residues: 42.6835 Evaluate side-chains 146 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8903 Z= 0.196 Angle : 0.562 10.640 12064 Z= 0.268 Chirality : 0.040 0.125 1387 Planarity : 0.003 0.053 1524 Dihedral : 5.121 68.826 1233 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 2.77 % Allowed : 20.47 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.26), residues: 1109 helix: 1.52 (0.29), residues: 352 sheet: -0.83 (0.30), residues: 287 loop : -1.73 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 116 TYR 0.034 0.001 TYR A 193 ARG 0.005 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.051 Fit side-chains REVERT: B 15 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8232 (ptpp) REVERT: B 291 ASP cc_start: 0.7572 (t0) cc_final: 0.7263 (t0) REVERT: D 242 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7981 (mtp85) REVERT: E 87 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7259 (mtt-85) REVERT: A 71 MET cc_start: 0.4000 (ttp) cc_final: 0.3281 (mmm) REVERT: A 131 LEU cc_start: 0.7769 (tp) cc_final: 0.7445 (tp) outliers start: 26 outliers final: 24 residues processed: 147 average time/residue: 0.2382 time to fit residues: 47.6866 Evaluate side-chains 152 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 0.0040 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8903 Z= 0.215 Angle : 0.587 11.572 12064 Z= 0.279 Chirality : 0.040 0.126 1387 Planarity : 0.004 0.083 1524 Dihedral : 5.125 70.261 1233 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.45 % Allowed : 21.22 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.66 (0.26), residues: 1109 helix: 1.56 (0.29), residues: 351 sheet: -0.82 (0.30), residues: 288 loop : -1.75 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 116 TYR 0.037 0.002 TYR A 193 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.930 Fit side-chains REVERT: B 15 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8231 (ptpp) REVERT: B 291 ASP cc_start: 0.7604 (t0) cc_final: 0.7300 (t0) REVERT: D 242 ARG cc_start: 0.8454 (mtt180) cc_final: 0.7994 (mtp85) REVERT: E 43 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7749 (mmtm) REVERT: E 73 ASP cc_start: 0.7918 (t70) cc_final: 0.7666 (t0) REVERT: E 87 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7208 (mtt-85) REVERT: A 71 MET cc_start: 0.4006 (ttp) cc_final: 0.3325 (mmm) REVERT: A 131 LEU cc_start: 0.7793 (tp) cc_final: 0.7474 (tp) REVERT: A 218 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 23 outliers final: 23 residues processed: 144 average time/residue: 0.2265 time to fit residues: 44.0623 Evaluate side-chains 147 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 111 optimal weight: 0.0020 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8903 Z= 0.163 Angle : 0.571 10.844 12064 Z= 0.269 Chirality : 0.039 0.126 1387 Planarity : 0.003 0.056 1524 Dihedral : 5.026 70.244 1233 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 2.35 % Allowed : 21.54 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1109 helix: 1.66 (0.29), residues: 351 sheet: -0.73 (0.30), residues: 288 loop : -1.70 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 264 HIS 0.002 0.001 HIS E 232 PHE 0.010 0.001 PHE A 116 TYR 0.042 0.001 TYR A 193 ARG 0.012 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.007 Fit side-chains REVERT: B 15 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8250 (ptpp) REVERT: B 291 ASP cc_start: 0.7599 (t0) cc_final: 0.7301 (t0) REVERT: D 242 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7964 (mtp85) REVERT: E 43 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7735 (mmtm) REVERT: E 87 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.7255 (mtt-85) REVERT: A 71 MET cc_start: 0.3982 (ttp) cc_final: 0.3296 (mmm) REVERT: A 131 LEU cc_start: 0.7761 (tp) cc_final: 0.7435 (tp) REVERT: A 218 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 22 outliers final: 21 residues processed: 143 average time/residue: 0.2261 time to fit residues: 44.1592 Evaluate side-chains 145 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.173353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120918 restraints weight = 19738.582| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.93 r_work: 0.3122 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8903 Z= 0.173 Angle : 0.580 11.457 12064 Z= 0.275 Chirality : 0.039 0.126 1387 Planarity : 0.003 0.055 1524 Dihedral : 4.995 70.816 1233 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 2.35 % Allowed : 21.75 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.26), residues: 1109 helix: 1.69 (0.29), residues: 351 sheet: -0.69 (0.31), residues: 288 loop : -1.66 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 264 HIS 0.003 0.001 HIS E 232 PHE 0.015 0.001 PHE A 116 TYR 0.043 0.001 TYR A 193 ARG 0.012 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2064.87 seconds wall clock time: 38 minutes 20.55 seconds (2300.55 seconds total)