Starting phenix.real_space_refine on Sat Feb 17 09:02:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w57_32316/02_2024/7w57_32316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w57_32316/02_2024/7w57_32316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w57_32316/02_2024/7w57_32316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w57_32316/02_2024/7w57_32316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w57_32316/02_2024/7w57_32316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w57_32316/02_2024/7w57_32316.pdb" } resolution = 3.2 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= 0.006 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 55 5.16 5 C 5859 2.51 5 N 1574 2.21 5 O 1682 1.98 5 H 9072 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 357": "OE1" <-> "OE2" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 265": "OE1" <-> "OE2" Residue "C ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 222": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 105": "OE1" <-> "OE2" Residue "R ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 295": "OE1" <-> "OE2" Residue "R ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18242 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3752 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 5074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5074 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 201 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 2, 'TRANS': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3502 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 831 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4882 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 14, 'TRANS': 282} Chain breaks: 1 Time building chain proxies: 7.78, per 1000 atoms: 0.43 Number of scatterers: 18242 At special positions: 0 Unit cell: (111.24, 130.68, 120.96, 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 55 16.00 O 1682 8.00 N 1574 7.00 C 5859 6.00 H 9072 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " 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: 14.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.652A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.124A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.963A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 11 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.767A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.583A pdb=" N ILE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 44 through 73 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 73 through 78 Processing helix chain 'R' and resid 81 through 108 Proline residue: R 100 - end of helix removed outlier: 3.569A pdb=" N TRP R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 150 through 158 removed outlier: 3.609A pdb=" N LYS R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 184 removed outlier: 3.542A pdb=" N LEU R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Proline residue: R 180 - end of helix Processing helix chain 'R' and resid 209 through 225 removed outlier: 3.685A pdb=" N PHE R 215 " --> pdb=" O TRP R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 245 Processing helix chain 'R' and resid 258 through 294 Proline residue: R 283 - end of helix removed outlier: 3.588A pdb=" N ARG R 288 " --> pdb=" O PHE R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 328 removed outlier: 3.581A pdb=" N SER R 320 " --> pdb=" O PHE R 316 " (cutoff:3.500A) Proline residue: R 324 - end of helix Processing helix chain 'R' and resid 331 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.212A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.889A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.593A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.780A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 6.349A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.728A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.636A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.636A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.975A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.975A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 5.834A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 185 through 189 484 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 14.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9045 1.02 - 1.22: 29 1.22 - 1.41: 3941 1.41 - 1.61: 5353 1.61 - 1.81: 81 Bond restraints: 18449 Sorted by residual: bond pdb=" SG CYS R 204 " pdb=" HG CYS R 204 " ideal model delta sigma weight residual 1.200 1.343 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" SG CYS R 119 " pdb=" HG CYS R 119 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" ND2 ASN B 298 " pdb="HD21 ASN B 298 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN B 298 " pdb="HD22 ASN B 298 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C ARG E 191 " pdb=" O ARG E 191 " ideal model delta sigma weight residual 1.234 1.164 0.070 1.19e-02 7.06e+03 3.49e+01 ... (remaining 18444 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.48: 261 106.48 - 113.36: 21164 113.36 - 120.24: 6229 120.24 - 127.12: 5424 127.12 - 134.00: 105 Bond angle restraints: 33183 Sorted by residual: angle pdb=" N ASP B 296 " pdb=" CA ASP B 296 " pdb=" C ASP B 296 " ideal model delta sigma weight residual 110.50 100.82 9.68 1.41e+00 5.03e-01 4.71e+01 angle pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" C ARG E 191 " ideal model delta sigma weight residual 108.42 99.60 8.82 1.54e+00 4.22e-01 3.28e+01 angle pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " ideal model delta sigma weight residual 115.38 123.02 -7.64 1.40e+00 5.10e-01 2.97e+01 angle pdb=" N ASP B 295 " pdb=" CA ASP B 295 " pdb=" C ASP B 295 " ideal model delta sigma weight residual 111.71 105.78 5.93 1.15e+00 7.56e-01 2.66e+01 angle pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" O ARG E 191 " ideal model delta sigma weight residual 121.10 116.25 4.85 1.10e+00 8.26e-01 1.94e+01 ... (remaining 33178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8085 17.91 - 35.82: 439 35.82 - 53.72: 125 53.72 - 71.63: 75 71.63 - 89.54: 8 Dihedral angle restraints: 8732 sinusoidal: 4656 harmonic: 4076 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 177.82 -84.82 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CA GLY B 315 " pdb=" C GLY B 315 " pdb=" N HIS B 316 " pdb=" CA HIS B 316 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1216 0.056 - 0.111: 176 0.111 - 0.167: 26 0.167 - 0.222: 1 0.222 - 0.277: 2 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CB VAL B 117 " pdb=" CA VAL B 117 " pdb=" CG1 VAL B 117 " pdb=" CG2 VAL B 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ASP B 296 " pdb=" N ASP B 296 " pdb=" C ASP B 296 " pdb=" CB ASP B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE R 187 " pdb=" N ILE R 187 " pdb=" C ILE R 187 " pdb=" CB ILE R 187 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1418 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 298 " -0.115 2.00e-02 2.50e+03 1.14e-01 1.95e+02 pdb=" CG ASN B 298 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 298 " 0.111 2.00e-02 2.50e+03 pdb=" ND2 ASN B 298 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 298 " 0.161 2.00e-02 2.50e+03 pdb="HD22 ASN B 298 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 274 " -0.011 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" N ILE B 275 " 0.035 2.00e-02 2.50e+03 pdb=" CA ILE B 275 " -0.009 2.00e-02 2.50e+03 pdb=" H ILE B 275 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 222 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C PHE R 222 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE R 222 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU R 223 " -0.011 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 673 2.16 - 2.77: 35380 2.77 - 3.38: 52521 3.38 - 3.99: 68488 3.99 - 4.60: 107225 Nonbonded interactions: 264287 Sorted by model distance: nonbonded pdb="HH11 ARG B 101 " pdb=" OE2 GLU B 143 " model vdw 1.548 1.850 nonbonded pdb=" HG1 THR B 279 " pdb=" O VAL B 320 " model vdw 1.550 1.850 nonbonded pdb=" OE1 GLU B 135 " pdb=" H GLU B 135 " model vdw 1.554 1.850 nonbonded pdb=" H PHE B 240 " pdb=" O ALA B 245 " model vdw 1.556 1.850 nonbonded pdb=" OD2 ASP B 259 " pdb=" H ALA B 262 " model vdw 1.568 1.850 ... (remaining 264282 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=0.00 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: 3.480 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: 3.910 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 57.680 Find NCS groups from input model: 0.320 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 0.070 9377 Z= 0.222 Angle : 0.578 9.677 12705 Z= 0.351 Chirality : 0.042 0.277 1421 Planarity : 0.003 0.029 1616 Dihedral : 11.438 89.541 3378 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.20 % Allowed : 3.99 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.24), residues: 1140 helix: 1.04 (0.24), residues: 405 sheet: 0.11 (0.31), residues: 283 loop : 0.33 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.006 0.001 HIS B 147 PHE 0.014 0.001 PHE R 338 TYR 0.015 0.001 TYR E 190 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8178 (mp0) cc_final: 0.7932 (mp0) REVERT: B 328 ASP cc_start: 0.8186 (p0) cc_final: 0.7848 (p0) REVERT: C 0 ARG cc_start: 0.7962 (mtt180) cc_final: 0.5184 (pmt170) REVERT: R 108 ARG cc_start: 0.7207 (mtp-110) cc_final: 0.6856 (tpt90) REVERT: R 227 LEU cc_start: 0.8638 (tp) cc_final: 0.8356 (mt) REVERT: R 306 ASN cc_start: 0.8139 (m-40) cc_final: 0.7910 (m-40) outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.6280 time to fit residues: 189.2413 Evaluate side-chains 175 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN E 38 GLN E 179 GLN E 183 GLN R 267 ASN R 339 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9377 Z= 0.208 Angle : 0.519 5.209 12705 Z= 0.282 Chirality : 0.041 0.153 1421 Planarity : 0.004 0.043 1616 Dihedral : 5.105 55.796 1266 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.00 % Allowed : 7.48 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.98 (0.25), residues: 1140 helix: 1.56 (0.25), residues: 410 sheet: 0.09 (0.30), residues: 289 loop : 0.35 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.004 0.001 HIS R 73 PHE 0.014 0.001 PHE R 338 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8087 (mtpp) REVERT: A 281 GLU cc_start: 0.8099 (mp0) cc_final: 0.7875 (mp0) REVERT: B 328 ASP cc_start: 0.8132 (p0) cc_final: 0.7587 (p0) REVERT: C 0 ARG cc_start: 0.7965 (mtt180) cc_final: 0.5316 (pmt170) REVERT: G 58 ASN cc_start: 0.7795 (t0) cc_final: 0.7471 (t0) REVERT: R 45 PHE cc_start: 0.7406 (t80) cc_final: 0.6866 (t80) REVERT: R 108 ARG cc_start: 0.7113 (mtp-110) cc_final: 0.6701 (tpt90) REVERT: R 293 PHE cc_start: 0.7672 (m-80) cc_final: 0.7386 (m-80) outliers start: 10 outliers final: 7 residues processed: 188 average time/residue: 0.5787 time to fit residues: 142.1237 Evaluate side-chains 175 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN G 23 ASN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 157 GLN R 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9377 Z= 0.285 Angle : 0.528 5.457 12705 Z= 0.286 Chirality : 0.041 0.141 1421 Planarity : 0.004 0.040 1616 Dihedral : 5.051 56.181 1266 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.40 % Allowed : 8.87 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.90 (0.25), residues: 1140 helix: 1.70 (0.25), residues: 410 sheet: -0.06 (0.30), residues: 290 loop : 0.15 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.003 0.001 HIS B 96 PHE 0.011 0.001 PHE R 338 TYR 0.018 0.001 TYR E 190 ARG 0.006 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8122 (mtpp) REVERT: B 239 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: C 0 ARG cc_start: 0.7933 (mtt180) cc_final: 0.5328 (pmt170) REVERT: R 45 PHE cc_start: 0.7505 (t80) cc_final: 0.6906 (t80) REVERT: R 108 ARG cc_start: 0.7445 (mtp-110) cc_final: 0.7013 (tpt90) REVERT: R 127 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7458 (mm-30) REVERT: R 157 GLN cc_start: 0.7296 (tt0) cc_final: 0.7082 (tt0) outliers start: 14 outliers final: 10 residues processed: 179 average time/residue: 0.6104 time to fit residues: 141.7542 Evaluate side-chains 172 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 225 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9377 Z= 0.257 Angle : 0.511 5.332 12705 Z= 0.275 Chirality : 0.041 0.142 1421 Planarity : 0.004 0.044 1616 Dihedral : 4.961 56.630 1266 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.30 % Allowed : 10.47 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.89 (0.25), residues: 1140 helix: 1.80 (0.25), residues: 410 sheet: -0.04 (0.31), residues: 276 loop : 0.00 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.004 0.001 HIS B 96 PHE 0.011 0.001 PHE R 338 TYR 0.017 0.001 TYR E 190 ARG 0.006 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8132 (mtpp) REVERT: B 239 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: C 0 ARG cc_start: 0.7939 (mtt180) cc_final: 0.5327 (pmt170) REVERT: E 140 MET cc_start: 0.8482 (mmm) cc_final: 0.8068 (mmm) REVERT: R 45 PHE cc_start: 0.7605 (t80) cc_final: 0.6994 (t80) REVERT: R 108 ARG cc_start: 0.7450 (mtp-110) cc_final: 0.7012 (tpt90) outliers start: 13 outliers final: 11 residues processed: 173 average time/residue: 0.6055 time to fit residues: 136.0309 Evaluate side-chains 173 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9377 Z= 0.308 Angle : 0.524 5.805 12705 Z= 0.283 Chirality : 0.041 0.142 1421 Planarity : 0.004 0.050 1616 Dihedral : 4.990 56.998 1266 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 11.37 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.81 (0.25), residues: 1140 helix: 1.79 (0.25), residues: 410 sheet: -0.05 (0.31), residues: 281 loop : -0.14 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.004 0.001 HIS B 316 PHE 0.012 0.001 PHE R 131 TYR 0.018 0.001 TYR E 190 ARG 0.006 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8222 (mtpp) REVERT: A 303 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7280 (ttp80) REVERT: B 239 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: C 0 ARG cc_start: 0.7940 (mtt180) cc_final: 0.5306 (pmt170) REVERT: E 140 MET cc_start: 0.8475 (mmm) cc_final: 0.7945 (mmm) REVERT: R 45 PHE cc_start: 0.7622 (t80) cc_final: 0.6988 (t80) REVERT: R 108 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7041 (tpt90) outliers start: 17 outliers final: 10 residues processed: 175 average time/residue: 0.5704 time to fit residues: 131.6263 Evaluate side-chains 170 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9377 Z= 0.220 Angle : 0.498 5.220 12705 Z= 0.267 Chirality : 0.040 0.142 1421 Planarity : 0.004 0.052 1616 Dihedral : 4.853 57.136 1266 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.50 % Allowed : 11.57 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.93 (0.25), residues: 1140 helix: 1.93 (0.25), residues: 411 sheet: 0.01 (0.31), residues: 280 loop : -0.11 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.003 0.001 HIS B 316 PHE 0.011 0.001 PHE R 338 TYR 0.016 0.001 TYR E 190 ARG 0.007 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8162 (mtpp) REVERT: A 303 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7266 (ttp80) REVERT: B 239 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8516 (m-80) REVERT: E 140 MET cc_start: 0.8447 (mmm) cc_final: 0.7909 (mmm) REVERT: R 45 PHE cc_start: 0.7593 (t80) cc_final: 0.6967 (t80) REVERT: R 108 ARG cc_start: 0.7484 (mtp-110) cc_final: 0.7018 (tpt90) REVERT: R 227 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8287 (mp) outliers start: 15 outliers final: 11 residues processed: 174 average time/residue: 0.5685 time to fit residues: 132.2994 Evaluate side-chains 174 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9377 Z= 0.301 Angle : 0.518 5.765 12705 Z= 0.279 Chirality : 0.041 0.141 1421 Planarity : 0.004 0.058 1616 Dihedral : 4.930 57.485 1266 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.60 % Allowed : 12.06 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.82 (0.25), residues: 1140 helix: 1.89 (0.25), residues: 411 sheet: -0.07 (0.31), residues: 280 loop : -0.21 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.004 0.001 HIS B 96 PHE 0.011 0.001 PHE B 246 TYR 0.018 0.001 TYR E 190 ARG 0.008 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8275 (mtpp) REVERT: A 303 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7291 (ttp80) REVERT: B 151 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 239 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: R 108 ARG cc_start: 0.7485 (mtp-110) cc_final: 0.7052 (tpt90) REVERT: R 110 TYR cc_start: 0.5902 (t80) cc_final: 0.5699 (m-80) REVERT: R 227 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8300 (mp) outliers start: 16 outliers final: 13 residues processed: 174 average time/residue: 0.5913 time to fit residues: 136.1238 Evaluate side-chains 175 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9377 Z= 0.148 Angle : 0.469 4.672 12705 Z= 0.249 Chirality : 0.040 0.145 1421 Planarity : 0.003 0.061 1616 Dihedral : 4.630 57.722 1266 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.30 % Allowed : 12.66 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.14 (0.25), residues: 1140 helix: 2.19 (0.25), residues: 411 sheet: 0.04 (0.31), residues: 280 loop : -0.03 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.002 0.001 HIS B 59 PHE 0.009 0.001 PHE R 338 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8150 (mtpp) REVERT: A 226 ASP cc_start: 0.7874 (t70) cc_final: 0.7655 (t70) REVERT: B 151 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8642 (tt) REVERT: B 239 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: R 45 PHE cc_start: 0.7545 (t80) cc_final: 0.6932 (t80) REVERT: R 108 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.6957 (tpt90) REVERT: R 227 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8276 (mp) outliers start: 13 outliers final: 5 residues processed: 182 average time/residue: 0.5640 time to fit residues: 135.9107 Evaluate side-chains 175 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9377 Z= 0.249 Angle : 0.495 6.111 12705 Z= 0.265 Chirality : 0.040 0.141 1421 Planarity : 0.004 0.055 1616 Dihedral : 4.704 58.329 1266 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.20 % Allowed : 12.96 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.05 (0.25), residues: 1140 helix: 2.17 (0.25), residues: 412 sheet: 0.03 (0.31), residues: 280 loop : -0.17 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.003 0.001 HIS B 316 PHE 0.010 0.001 PHE R 338 TYR 0.017 0.001 TYR E 190 ARG 0.008 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8190 (mtpp) REVERT: A 217 ASP cc_start: 0.7253 (t0) cc_final: 0.7022 (t0) REVERT: A 226 ASP cc_start: 0.7975 (t70) cc_final: 0.7634 (t70) REVERT: B 151 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8688 (tt) REVERT: B 239 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: R 104 TYR cc_start: 0.8164 (t80) cc_final: 0.7820 (t80) REVERT: R 108 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.6982 (tpt90) REVERT: R 227 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8303 (mp) outliers start: 12 outliers final: 7 residues processed: 174 average time/residue: 0.5584 time to fit residues: 128.5178 Evaluate side-chains 172 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 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 273 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9377 Z= 0.137 Angle : 0.461 4.801 12705 Z= 0.245 Chirality : 0.039 0.157 1421 Planarity : 0.003 0.055 1616 Dihedral : 4.482 58.729 1266 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.00 % Allowed : 12.96 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1140 helix: 2.37 (0.25), residues: 412 sheet: 0.08 (0.31), residues: 280 loop : 0.02 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.003 0.001 HIS B 59 PHE 0.010 0.001 PHE R 338 TYR 0.013 0.001 TYR E 190 ARG 0.008 0.000 ARG R 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8145 (mtpp) REVERT: A 217 ASP cc_start: 0.7053 (t0) cc_final: 0.6783 (t0) REVERT: B 151 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 239 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: R 45 PHE cc_start: 0.7543 (t80) cc_final: 0.6962 (t80) REVERT: R 104 TYR cc_start: 0.8046 (t80) cc_final: 0.7741 (t80) REVERT: R 108 ARG cc_start: 0.7360 (mtp-110) cc_final: 0.6897 (tpt90) REVERT: R 227 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8286 (mp) REVERT: R 265 SER cc_start: 0.7254 (t) cc_final: 0.6937 (p) outliers start: 10 outliers final: 6 residues processed: 181 average time/residue: 0.5647 time to fit residues: 136.8377 Evaluate side-chains 178 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114118 restraints weight = 33324.133| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.30 r_work: 0.2982 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9377 Z= 0.157 Angle : 0.466 4.906 12705 Z= 0.246 Chirality : 0.039 0.142 1421 Planarity : 0.003 0.051 1616 Dihedral : 4.451 59.229 1266 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.90 % Allowed : 13.26 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.35 (0.25), residues: 1140 helix: 2.43 (0.25), residues: 412 sheet: 0.16 (0.31), residues: 278 loop : 0.01 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.002 0.001 HIS B 59 PHE 0.009 0.001 PHE R 338 TYR 0.014 0.001 TYR E 190 ARG 0.008 0.000 ARG R 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4872.76 seconds wall clock time: 87 minutes 31.15 seconds (5251.15 seconds total)