Starting phenix.real_space_refine on Tue Sep 24 21:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/09_2024/8hcq_34663_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/09_2024/8hcq_34663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/09_2024/8hcq_34663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/09_2024/8hcq_34663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/09_2024/8hcq_34663_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/09_2024/8hcq_34663_neut.cif" } resolution = 3.01 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= 0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5725 2.51 5 N 1526 2.21 5 O 1673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8991 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1687 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 410 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2363 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 5.40, per 1000 atoms: 0.60 Number of scatterers: 8991 At special positions: 0 Unit cell: (107.944, 112.888, 126.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1673 8.00 N 1526 7.00 C 5725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.560A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.539A pdb=" N ALA A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.989A pdb=" N THR A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.558A pdb=" N LEU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.521A pdb=" N GLU B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.997A 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 220 through 224 Processing helix chain 'G' and resid 7 through 25 removed outlier: 4.406A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.610A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.726A pdb=" N VAL L 12 " --> pdb=" O ASP L 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 109 removed outlier: 3.529A pdb=" N TYR R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL R 96 " --> pdb=" O ILE R 92 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 143 Proline residue: R 135 - end of helix removed outlier: 3.516A pdb=" N PHE R 139 " --> pdb=" O PRO R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 159 removed outlier: 3.806A pdb=" N VAL R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 189 Processing helix chain 'R' and resid 199 through 222 removed outlier: 3.678A pdb=" N VAL R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Proline residue: R 219 - end of helix removed outlier: 3.971A pdb=" N ILE R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 254 through 264 Processing helix chain 'R' and resid 264 through 283 removed outlier: 3.836A pdb=" N VAL R 269 " --> pdb=" O CYS R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 330 Proline residue: R 321 - end of helix removed outlier: 3.783A pdb=" N ARG R 326 " --> pdb=" O LEU R 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS R 330 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 373 removed outlier: 3.812A pdb=" N LEU R 343 " --> pdb=" O ASN R 339 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE R 346 " --> pdb=" O GLU R 342 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.792A pdb=" N LEU R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.525A pdb=" N PHE A 187 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 252 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N HIS A 327 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 254 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 removed outlier: 6.717A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.930A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 93 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.924A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.970A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.471A 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 Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.776A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 257 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.579A pdb=" N ALA B 292 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.860A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.869A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.653A 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: 5.869A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.294A 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: 4.076A pdb=" N VAL E 147 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 230 through 231 removed outlier: 4.079A pdb=" N TYR R 231 " --> pdb=" O GLU R 234 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU R 234 " --> pdb=" O TYR R 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 402 hydrogen bonds defined for protein. 1140 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: 2.51 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2904 1.34 - 1.46: 2087 1.46 - 1.58: 4095 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9180 Sorted by residual: bond pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.41e+01 bond pdb=" N LYS R 377 " pdb=" CA LYS R 377 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.33e+00 bond pdb=" C MET R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.79e+00 bond pdb=" N MET E 92 " pdb=" CA MET E 92 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" C MET E 92 " pdb=" N TYR E 93 " ideal model delta sigma weight residual 1.330 1.310 0.019 1.32e-02 5.74e+03 2.17e+00 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 12282 2.57 - 5.14: 149 5.14 - 7.71: 17 7.71 - 10.28: 1 10.28 - 12.85: 1 Bond angle restraints: 12450 Sorted by residual: angle pdb=" C ARG R 340 " pdb=" CA ARG R 340 " pdb=" CB ARG R 340 " ideal model delta sigma weight residual 116.34 110.69 5.65 1.40e+00 5.10e-01 1.63e+01 angle pdb=" C SER L 4 " pdb=" N SER L 5 " pdb=" CA SER L 5 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA MET R 266 " pdb=" CB MET R 266 " pdb=" CG MET R 266 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" O ASP A 204 " pdb=" C ASP A 204 " pdb=" N GLU A 205 " ideal model delta sigma weight residual 123.29 119.66 3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 4651 16.30 - 32.59: 554 32.59 - 48.89: 178 48.89 - 65.19: 37 65.19 - 81.49: 8 Dihedral angle restraints: 5428 sinusoidal: 2071 harmonic: 3357 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 15 " pdb=" CB CYS L 15 " ideal model delta sinusoidal sigma weight residual -86.00 -127.39 41.39 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CG ARG A 230 " pdb=" CD ARG A 230 " pdb=" NE ARG A 230 " pdb=" CZ ARG A 230 " ideal model delta sinusoidal sigma weight residual 90.00 41.36 48.64 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA GLN B 264 " pdb=" C GLN B 264 " pdb=" N GLU B 265 " pdb=" CA GLU B 265 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 910 0.029 - 0.059: 324 0.059 - 0.088: 105 0.088 - 0.118: 66 0.118 - 0.147: 11 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA MET E 92 " pdb=" N MET E 92 " pdb=" C MET E 92 " pdb=" CB MET E 92 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ASN E 76 " pdb=" N ASN E 76 " pdb=" C ASN E 76 " pdb=" CB ASN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE R 196 " pdb=" N ILE R 196 " pdb=" C ILE R 196 " pdb=" CB ILE R 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1413 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 339 " -0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ASN R 339 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN R 339 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG R 340 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 198 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO R 199 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO R 199 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 199 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 204 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C ASP A 204 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP A 204 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 10 2.27 - 2.93: 3874 2.93 - 3.58: 12956 3.58 - 4.24: 19861 4.24 - 4.90: 33518 Nonbonded interactions: 70219 Sorted by model distance: nonbonded pdb=" CE1 HIS A 195 " pdb=" CE1 PHE A 197 " model vdw 1.609 3.560 nonbonded pdb=" ND1 HIS A 195 " pdb=" CE1 PHE A 197 " model vdw 2.019 3.420 nonbonded pdb=" OD2 ASP B 32 " pdb=" OG SER G 31 " model vdw 2.191 3.040 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.204 3.040 ... (remaining 70214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.870 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.790 Find NCS groups from input model: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 0.060 9180 Z= 0.178 Angle : 0.662 12.855 12450 Z= 0.353 Chirality : 0.039 0.147 1416 Planarity : 0.005 0.077 1580 Dihedral : 16.120 81.487 3250 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 0.21 % Allowed : 29.47 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1131 helix: 1.42 (0.28), residues: 371 sheet: 0.87 (0.33), residues: 268 loop : -0.94 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 68 HIS 0.013 0.001 HIS A 322 PHE 0.020 0.001 PHE E 212 TYR 0.012 0.001 TYR E 235 ARG 0.014 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.044 Fit side-chains REVERT: A 35 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7138 (mtm180) REVERT: B 13 ARG cc_start: 0.6661 (mpp80) cc_final: 0.6292 (mpp80) REVERT: B 175 ASP cc_start: 0.7093 (m-30) cc_final: 0.6882 (m-30) REVERT: B 202 ARG cc_start: 0.7003 (tpp-160) cc_final: 0.6266 (tpt170) REVERT: B 334 THR cc_start: 0.8198 (t) cc_final: 0.7796 (p) REVERT: R 181 VAL cc_start: 0.7129 (t) cc_final: 0.6865 (t) REVERT: R 212 LEU cc_start: 0.7808 (tm) cc_final: 0.7589 (tp) REVERT: R 224 PHE cc_start: 0.6646 (t80) cc_final: 0.5107 (t80) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2204 time to fit residues: 50.0274 Evaluate side-chains 147 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 102 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 342 ASN A 352 ASN B 93 ASN B 160 ASN B 181 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9180 Z= 0.374 Angle : 0.709 11.108 12450 Z= 0.372 Chirality : 0.047 0.202 1416 Planarity : 0.005 0.070 1580 Dihedral : 4.595 18.162 1244 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.16 % Favored : 95.67 % Rotamer: Outliers : 6.41 % Allowed : 22.03 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1131 helix: 1.08 (0.27), residues: 382 sheet: 0.61 (0.32), residues: 267 loop : -0.94 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.006 0.001 HIS B 230 PHE 0.025 0.003 PHE L 14 TYR 0.017 0.002 TYR E 235 ARG 0.007 0.001 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 204 time to evaluate : 1.132 Fit side-chains REVERT: A 188 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: A 254 LEU cc_start: 0.8105 (mm) cc_final: 0.7807 (mp) REVERT: B 13 ARG cc_start: 0.6638 (mpp80) cc_final: 0.6156 (mpp80) REVERT: B 79 SER cc_start: 0.8140 (p) cc_final: 0.7933 (p) REVERT: B 165 SER cc_start: 0.7928 (t) cc_final: 0.7648 (p) REVERT: B 173 LEU cc_start: 0.7972 (tt) cc_final: 0.7638 (tp) REVERT: B 188 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7644 (m-70) REVERT: B 217 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7490 (t0) REVERT: B 259 ASP cc_start: 0.7436 (t70) cc_final: 0.7055 (t0) REVERT: B 261 ARG cc_start: 0.8212 (mtm180) cc_final: 0.7809 (mtp180) REVERT: B 266 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7577 (mp) REVERT: B 300 ASN cc_start: 0.7166 (m-40) cc_final: 0.6958 (m110) REVERT: B 308 ASP cc_start: 0.7494 (m-30) cc_final: 0.7171 (m-30) REVERT: B 317 ASP cc_start: 0.7566 (m-30) cc_final: 0.7355 (m-30) REVERT: B 334 THR cc_start: 0.8097 (t) cc_final: 0.7714 (p) REVERT: E 66 ARG cc_start: 0.7358 (ttp80) cc_final: 0.6608 (ttp80) REVERT: E 82 MET cc_start: 0.7576 (mmt) cc_final: 0.7164 (mmt) REVERT: E 102 TYR cc_start: 0.7907 (t80) cc_final: 0.7478 (t80) REVERT: E 107 PHE cc_start: 0.8526 (m-80) cc_final: 0.8002 (m-80) REVERT: R 108 ASN cc_start: 0.7354 (t0) cc_final: 0.6868 (t0) REVERT: R 181 VAL cc_start: 0.7052 (t) cc_final: 0.6820 (t) REVERT: R 240 MET cc_start: 0.7775 (pmm) cc_final: 0.7452 (pmm) REVERT: R 252 GLN cc_start: 0.6109 (tp40) cc_final: 0.5860 (tp40) REVERT: R 255 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6286 (tttm) REVERT: R 330 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7674 (mttp) outliers start: 62 outliers final: 39 residues processed: 242 average time/residue: 0.2515 time to fit residues: 80.9436 Evaluate side-chains 226 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 239 CYS Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET 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: 1.9990 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN G 44 HIS R 165 GLN R 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9180 Z= 0.230 Angle : 0.591 7.145 12450 Z= 0.307 Chirality : 0.043 0.173 1416 Planarity : 0.004 0.053 1580 Dihedral : 4.273 17.854 1244 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 6.41 % Allowed : 22.85 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1131 helix: 1.31 (0.27), residues: 382 sheet: 0.67 (0.33), residues: 255 loop : -0.97 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.010 0.001 HIS G 44 PHE 0.011 0.002 PHE A 187 TYR 0.016 0.001 TYR E 235 ARG 0.004 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 189 time to evaluate : 1.153 Fit side-chains REVERT: A 46 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6251 (mptm) REVERT: A 188 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: B 13 ARG cc_start: 0.6704 (mpp80) cc_final: 0.6229 (mpp80) REVERT: B 79 SER cc_start: 0.8240 (p) cc_final: 0.8028 (p) REVERT: B 165 SER cc_start: 0.7829 (t) cc_final: 0.7437 (p) REVERT: B 170 THR cc_start: 0.6545 (t) cc_final: 0.5336 (m) REVERT: B 173 LEU cc_start: 0.8015 (tt) cc_final: 0.7807 (tt) REVERT: B 188 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7724 (m-70) REVERT: B 202 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.7025 (tpp-160) REVERT: B 215 LEU cc_start: 0.7390 (tp) cc_final: 0.7025 (tp) REVERT: B 259 ASP cc_start: 0.7431 (t70) cc_final: 0.7035 (t0) REVERT: B 261 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7807 (mtp180) REVERT: B 266 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7604 (mp) REVERT: B 308 ASP cc_start: 0.7440 (m-30) cc_final: 0.7131 (m-30) REVERT: B 317 ASP cc_start: 0.7570 (m-30) cc_final: 0.7351 (m-30) REVERT: B 334 THR cc_start: 0.8083 (t) cc_final: 0.7742 (p) REVERT: E 66 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6593 (ttp80) REVERT: E 82 MET cc_start: 0.7753 (mmt) cc_final: 0.7182 (mmt) REVERT: E 102 TYR cc_start: 0.7913 (t80) cc_final: 0.7575 (t80) REVERT: R 86 ILE cc_start: 0.5285 (pt) cc_final: 0.5078 (pt) REVERT: R 108 ASN cc_start: 0.7369 (t0) cc_final: 0.6819 (t0) REVERT: R 181 VAL cc_start: 0.7059 (t) cc_final: 0.6841 (t) REVERT: R 330 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7709 (mtpp) outliers start: 62 outliers final: 43 residues processed: 231 average time/residue: 0.2577 time to fit residues: 77.7547 Evaluate side-chains 231 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 239 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9180 Z= 0.177 Angle : 0.559 9.451 12450 Z= 0.289 Chirality : 0.041 0.154 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.071 17.500 1244 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 5.58 % Allowed : 24.10 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1131 helix: 1.58 (0.27), residues: 372 sheet: 0.74 (0.33), residues: 253 loop : -0.96 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.006 0.001 HIS G 44 PHE 0.012 0.001 PHE A 187 TYR 0.015 0.001 TYR E 235 ARG 0.006 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6720 (mtm110) cc_final: 0.6401 (mtm110) REVERT: A 46 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6108 (mptm) REVERT: A 188 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: B 84 LEU cc_start: 0.8164 (mt) cc_final: 0.7834 (mt) REVERT: B 165 SER cc_start: 0.7788 (t) cc_final: 0.7408 (p) REVERT: B 166 SER cc_start: 0.7349 (OUTLIER) cc_final: 0.6932 (p) REVERT: B 170 THR cc_start: 0.6452 (t) cc_final: 0.5198 (m) REVERT: B 188 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7757 (m-70) REVERT: B 215 LEU cc_start: 0.7370 (tp) cc_final: 0.7047 (tp) REVERT: B 259 ASP cc_start: 0.7422 (t70) cc_final: 0.7010 (t0) REVERT: B 261 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7761 (mtp180) REVERT: B 266 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 308 ASP cc_start: 0.7444 (m-30) cc_final: 0.7136 (m-30) REVERT: B 317 ASP cc_start: 0.7570 (m-30) cc_final: 0.7336 (m-30) REVERT: B 334 THR cc_start: 0.8051 (t) cc_final: 0.7736 (p) REVERT: E 66 ARG cc_start: 0.7218 (ttp80) cc_final: 0.6632 (ttp80) REVERT: E 82 MET cc_start: 0.7762 (mmt) cc_final: 0.7088 (mmm) REVERT: E 102 TYR cc_start: 0.7868 (t80) cc_final: 0.7581 (t80) REVERT: R 108 ASN cc_start: 0.7357 (t0) cc_final: 0.6749 (t0) REVERT: R 137 ASN cc_start: 0.7097 (m-40) cc_final: 0.6792 (m-40) REVERT: R 220 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6830 (tm-30) outliers start: 54 outliers final: 42 residues processed: 213 average time/residue: 0.2600 time to fit residues: 72.4579 Evaluate side-chains 225 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9180 Z= 0.151 Angle : 0.537 8.732 12450 Z= 0.277 Chirality : 0.041 0.154 1416 Planarity : 0.004 0.055 1580 Dihedral : 3.919 18.014 1244 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 6.00 % Allowed : 23.58 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1131 helix: 1.63 (0.27), residues: 374 sheet: 0.73 (0.33), residues: 253 loop : -0.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.010 0.001 HIS G 44 PHE 0.012 0.001 PHE A 187 TYR 0.014 0.001 TYR E 235 ARG 0.006 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6720 (mtm110) cc_final: 0.6405 (mtm110) REVERT: A 46 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6082 (mptm) REVERT: A 188 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: A 196 MET cc_start: 0.7636 (tpp) cc_final: 0.7277 (ttt) REVERT: A 249 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 307 ARG cc_start: 0.6183 (ttm-80) cc_final: 0.5842 (ttm-80) REVERT: B 73 ARG cc_start: 0.8204 (ttt180) cc_final: 0.7785 (ttt180) REVERT: B 84 LEU cc_start: 0.8151 (mt) cc_final: 0.7819 (mt) REVERT: B 165 SER cc_start: 0.7786 (t) cc_final: 0.7421 (p) REVERT: B 188 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.7771 (m-70) REVERT: B 202 ARG cc_start: 0.7385 (tpp80) cc_final: 0.7147 (ttm-80) REVERT: B 215 LEU cc_start: 0.7327 (tp) cc_final: 0.7004 (tp) REVERT: B 259 ASP cc_start: 0.7415 (t70) cc_final: 0.6998 (t0) REVERT: B 261 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7877 (mtp180) REVERT: B 266 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 308 ASP cc_start: 0.7451 (m-30) cc_final: 0.7143 (m-30) REVERT: B 334 THR cc_start: 0.8044 (t) cc_final: 0.7732 (p) REVERT: E 66 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6503 (ttp80) REVERT: E 82 MET cc_start: 0.7705 (mmt) cc_final: 0.7096 (mmm) REVERT: E 102 TYR cc_start: 0.7835 (t80) cc_final: 0.7052 (t80) REVERT: E 224 VAL cc_start: 0.7884 (t) cc_final: 0.7594 (p) REVERT: R 91 PHE cc_start: 0.7401 (t80) cc_final: 0.7191 (t80) REVERT: R 108 ASN cc_start: 0.7344 (t0) cc_final: 0.6719 (t0) REVERT: R 137 ASN cc_start: 0.7052 (m-40) cc_final: 0.6749 (m-40) REVERT: R 220 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: R 224 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.5920 (t80) REVERT: R 262 PHE cc_start: 0.7016 (t80) cc_final: 0.6766 (t80) outliers start: 58 outliers final: 40 residues processed: 215 average time/residue: 0.2664 time to fit residues: 74.9747 Evaluate side-chains 223 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9180 Z= 0.211 Angle : 0.563 7.730 12450 Z= 0.290 Chirality : 0.042 0.155 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.029 17.112 1244 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.54 % Favored : 96.29 % Rotamer: Outliers : 6.00 % Allowed : 24.51 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1131 helix: 1.53 (0.27), residues: 379 sheet: 0.67 (0.32), residues: 265 loop : -0.95 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.016 0.001 HIS G 44 PHE 0.012 0.001 PHE A 187 TYR 0.015 0.001 TYR E 235 ARG 0.007 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 192 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6804 (mtm110) cc_final: 0.6491 (mtm110) REVERT: A 46 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6334 (mptm) REVERT: A 188 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: A 196 MET cc_start: 0.7678 (tpp) cc_final: 0.7372 (ttt) REVERT: A 215 ASP cc_start: 0.7295 (t0) cc_final: 0.6870 (t0) REVERT: A 249 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8086 (p) REVERT: A 254 LEU cc_start: 0.8144 (mm) cc_final: 0.7865 (mt) REVERT: A 347 ILE cc_start: 0.7778 (tp) cc_final: 0.7484 (mt) REVERT: B 73 ARG cc_start: 0.8318 (ttt180) cc_final: 0.7838 (ttt180) REVERT: B 84 LEU cc_start: 0.8183 (mt) cc_final: 0.7856 (mt) REVERT: B 165 SER cc_start: 0.7726 (t) cc_final: 0.7383 (p) REVERT: B 170 THR cc_start: 0.6499 (t) cc_final: 0.5273 (m) REVERT: B 188 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7844 (m-70) REVERT: B 202 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6773 (mmm160) REVERT: B 215 LEU cc_start: 0.7422 (tp) cc_final: 0.7049 (tp) REVERT: B 259 ASP cc_start: 0.7439 (t70) cc_final: 0.6982 (t0) REVERT: B 261 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7757 (mtp180) REVERT: B 308 ASP cc_start: 0.7460 (m-30) cc_final: 0.7181 (m-30) REVERT: B 334 THR cc_start: 0.8048 (t) cc_final: 0.7737 (p) REVERT: E 66 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6548 (ttp80) REVERT: E 82 MET cc_start: 0.7733 (mmt) cc_final: 0.7198 (mmt) REVERT: E 102 TYR cc_start: 0.7867 (t80) cc_final: 0.7005 (t80) REVERT: E 224 VAL cc_start: 0.7976 (t) cc_final: 0.7694 (p) REVERT: R 108 ASN cc_start: 0.7391 (t0) cc_final: 0.6753 (t0) REVERT: R 137 ASN cc_start: 0.7107 (m-40) cc_final: 0.6820 (m-40) REVERT: R 220 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: R 224 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.5934 (t80) REVERT: R 262 PHE cc_start: 0.7056 (t80) cc_final: 0.6821 (t80) outliers start: 58 outliers final: 43 residues processed: 225 average time/residue: 0.2495 time to fit residues: 74.2549 Evaluate side-chains 242 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9180 Z= 0.270 Angle : 0.617 10.121 12450 Z= 0.314 Chirality : 0.044 0.175 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.235 16.891 1244 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 6.10 % Allowed : 24.61 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1131 helix: 1.37 (0.27), residues: 378 sheet: 0.54 (0.32), residues: 268 loop : -1.00 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 216 HIS 0.024 0.002 HIS G 44 PHE 0.013 0.002 PHE B 239 TYR 0.016 0.002 TYR E 235 ARG 0.010 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 1.020 Fit side-chains REVERT: A 24 ARG cc_start: 0.6844 (mtm110) cc_final: 0.6500 (mtm110) REVERT: A 46 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6680 (mptm) REVERT: A 196 MET cc_start: 0.7711 (tpp) cc_final: 0.7380 (ttt) REVERT: A 249 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 254 LEU cc_start: 0.8247 (mm) cc_final: 0.7990 (mt) REVERT: A 338 ARG cc_start: 0.7460 (mmm160) cc_final: 0.7242 (ttm-80) REVERT: A 347 ILE cc_start: 0.7802 (tp) cc_final: 0.7493 (mt) REVERT: A 357 ASN cc_start: 0.7868 (m110) cc_final: 0.7630 (m110) REVERT: B 13 ARG cc_start: 0.6610 (mpp80) cc_final: 0.6196 (mpp80) REVERT: B 73 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7976 (ttt180) REVERT: B 84 LEU cc_start: 0.8205 (mt) cc_final: 0.7884 (mt) REVERT: B 165 SER cc_start: 0.7682 (t) cc_final: 0.7342 (p) REVERT: B 170 THR cc_start: 0.6678 (t) cc_final: 0.5478 (m) REVERT: B 176 ILE cc_start: 0.7043 (mm) cc_final: 0.6808 (mt) REVERT: B 188 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.7840 (m-70) REVERT: B 202 ARG cc_start: 0.7345 (tpp80) cc_final: 0.7094 (ttm-80) REVERT: B 259 ASP cc_start: 0.7498 (t70) cc_final: 0.7067 (t0) REVERT: B 261 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7950 (mtm180) REVERT: B 308 ASP cc_start: 0.7490 (m-30) cc_final: 0.7235 (m-30) REVERT: B 334 THR cc_start: 0.8081 (t) cc_final: 0.7801 (p) REVERT: E 82 MET cc_start: 0.7796 (mmt) cc_final: 0.7212 (mmm) REVERT: E 102 TYR cc_start: 0.7974 (t80) cc_final: 0.7255 (t80) REVERT: E 224 VAL cc_start: 0.8033 (t) cc_final: 0.7757 (p) REVERT: R 108 ASN cc_start: 0.7386 (t0) cc_final: 0.6746 (t0) REVERT: R 137 ASN cc_start: 0.7119 (m-40) cc_final: 0.6860 (m-40) REVERT: R 220 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: R 224 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.5963 (t80) REVERT: R 241 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6724 (tt) outliers start: 59 outliers final: 45 residues processed: 232 average time/residue: 0.2816 time to fit residues: 85.2375 Evaluate side-chains 242 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 191 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9180 Z= 0.224 Angle : 0.590 11.312 12450 Z= 0.302 Chirality : 0.043 0.159 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.187 17.253 1244 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 6.00 % Allowed : 24.82 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1131 helix: 1.30 (0.27), residues: 381 sheet: 0.45 (0.32), residues: 270 loop : -0.94 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.005 0.001 HIS G 44 PHE 0.036 0.002 PHE R 91 TYR 0.015 0.001 TYR E 235 ARG 0.010 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 1.059 Fit side-chains REVERT: A 46 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6599 (mptm) REVERT: A 215 ASP cc_start: 0.7311 (t0) cc_final: 0.6887 (t0) REVERT: A 249 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8017 (p) REVERT: A 254 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 298 ARG cc_start: 0.8220 (mtp180) cc_final: 0.8020 (mtp85) REVERT: A 347 ILE cc_start: 0.7786 (tp) cc_final: 0.7474 (mt) REVERT: A 354 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.7246 (ttm-80) REVERT: A 357 ASN cc_start: 0.7786 (m110) cc_final: 0.7522 (m110) REVERT: B 13 ARG cc_start: 0.6624 (mpp80) cc_final: 0.6211 (mpp80) REVERT: B 73 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7961 (ttt180) REVERT: B 84 LEU cc_start: 0.8175 (mt) cc_final: 0.7841 (mt) REVERT: B 165 SER cc_start: 0.7660 (t) cc_final: 0.7336 (p) REVERT: B 170 THR cc_start: 0.6640 (t) cc_final: 0.5440 (m) REVERT: B 175 ASP cc_start: 0.7399 (m-30) cc_final: 0.7123 (t0) REVERT: B 176 ILE cc_start: 0.7041 (mm) cc_final: 0.6475 (mt) REVERT: B 188 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7861 (m-70) REVERT: B 202 ARG cc_start: 0.7314 (tpp80) cc_final: 0.7039 (ttm-80) REVERT: B 259 ASP cc_start: 0.7554 (t70) cc_final: 0.7305 (t0) REVERT: B 308 ASP cc_start: 0.7454 (m-30) cc_final: 0.7212 (m-30) REVERT: E 82 MET cc_start: 0.7780 (mmt) cc_final: 0.7225 (mmm) REVERT: E 102 TYR cc_start: 0.7965 (t80) cc_final: 0.7226 (t80) REVERT: E 140 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7233 (mtm) REVERT: E 224 VAL cc_start: 0.8031 (t) cc_final: 0.7768 (p) REVERT: R 108 ASN cc_start: 0.7376 (t0) cc_final: 0.6726 (t0) REVERT: R 137 ASN cc_start: 0.7105 (m-40) cc_final: 0.6844 (m-40) REVERT: R 220 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: R 224 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.5926 (t80) outliers start: 58 outliers final: 43 residues processed: 230 average time/residue: 0.2554 time to fit residues: 77.1395 Evaluate side-chains 244 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.6980 chunk 104 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 107 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9180 Z= 0.228 Angle : 0.604 11.914 12450 Z= 0.310 Chirality : 0.043 0.160 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.207 17.492 1244 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.84 % Rotamer: Outliers : 5.79 % Allowed : 25.65 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1131 helix: 1.27 (0.27), residues: 381 sheet: 0.45 (0.32), residues: 270 loop : -0.92 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.009 0.001 HIS G 44 PHE 0.013 0.002 PHE B 239 TYR 0.020 0.001 TYR E 235 ARG 0.011 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 191 time to evaluate : 1.055 Fit side-chains REVERT: A 20 ASP cc_start: 0.7706 (m-30) cc_final: 0.7503 (m-30) REVERT: A 46 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6613 (mptm) REVERT: A 215 ASP cc_start: 0.7313 (t0) cc_final: 0.6887 (t0) REVERT: A 249 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 254 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7981 (mt) REVERT: A 298 ARG cc_start: 0.8221 (mtp180) cc_final: 0.8014 (mtp85) REVERT: A 347 ILE cc_start: 0.7789 (tp) cc_final: 0.7455 (mt) REVERT: A 357 ASN cc_start: 0.7809 (m110) cc_final: 0.7546 (m110) REVERT: B 13 ARG cc_start: 0.6619 (mpp80) cc_final: 0.6211 (mpp80) REVERT: B 84 LEU cc_start: 0.8177 (mt) cc_final: 0.7843 (mt) REVERT: B 165 SER cc_start: 0.7648 (t) cc_final: 0.7328 (p) REVERT: B 170 THR cc_start: 0.6651 (t) cc_final: 0.5456 (m) REVERT: B 175 ASP cc_start: 0.7381 (m-30) cc_final: 0.7131 (t0) REVERT: B 176 ILE cc_start: 0.7114 (mm) cc_final: 0.6657 (mt) REVERT: B 188 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7886 (m-70) REVERT: B 202 ARG cc_start: 0.7311 (tpp80) cc_final: 0.7022 (ttm-80) REVERT: B 259 ASP cc_start: 0.7674 (t70) cc_final: 0.7450 (t0) REVERT: B 266 LEU cc_start: 0.8004 (mt) cc_final: 0.7755 (mp) REVERT: B 308 ASP cc_start: 0.7449 (m-30) cc_final: 0.7204 (m-30) REVERT: E 82 MET cc_start: 0.7804 (mmt) cc_final: 0.7145 (mmm) REVERT: E 102 TYR cc_start: 0.7964 (t80) cc_final: 0.7656 (t80) REVERT: E 140 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: E 224 VAL cc_start: 0.8056 (t) cc_final: 0.7813 (p) REVERT: R 108 ASN cc_start: 0.7356 (t0) cc_final: 0.6705 (t0) REVERT: R 137 ASN cc_start: 0.7105 (m-40) cc_final: 0.6856 (m-40) REVERT: R 220 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: R 224 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.5913 (t80) REVERT: R 367 ILE cc_start: 0.6765 (pt) cc_final: 0.6498 (mt) outliers start: 56 outliers final: 44 residues processed: 223 average time/residue: 0.2627 time to fit residues: 76.9260 Evaluate side-chains 240 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 175 ASN ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9180 Z= 0.276 Angle : 0.637 11.716 12450 Z= 0.323 Chirality : 0.044 0.158 1416 Planarity : 0.004 0.053 1580 Dihedral : 4.318 17.417 1244 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.16 % Favored : 95.67 % Rotamer: Outliers : 5.58 % Allowed : 26.47 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1131 helix: 1.21 (0.27), residues: 381 sheet: 0.46 (0.32), residues: 267 loop : -0.94 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.013 0.002 HIS G 44 PHE 0.014 0.002 PHE B 239 TYR 0.021 0.002 TYR E 235 ARG 0.012 0.001 ARG A 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 190 time to evaluate : 1.014 Fit side-chains REVERT: A 249 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7979 (p) REVERT: A 254 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 298 ARG cc_start: 0.8232 (mtp180) cc_final: 0.8028 (mtp85) REVERT: A 347 ILE cc_start: 0.7781 (tp) cc_final: 0.7457 (mt) REVERT: A 354 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7144 (ttm-80) REVERT: B 13 ARG cc_start: 0.6622 (mpp80) cc_final: 0.6216 (mpp80) REVERT: B 24 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7114 (ttp-110) REVERT: B 50 MET cc_start: 0.7949 (mtp) cc_final: 0.7718 (ttm) REVERT: B 84 LEU cc_start: 0.8184 (mt) cc_final: 0.7844 (mt) REVERT: B 135 GLU cc_start: 0.7859 (mp0) cc_final: 0.7346 (mp0) REVERT: B 165 SER cc_start: 0.7620 (t) cc_final: 0.7307 (p) REVERT: B 170 THR cc_start: 0.6736 (t) cc_final: 0.5561 (m) REVERT: B 175 ASP cc_start: 0.7426 (m-30) cc_final: 0.7189 (t0) REVERT: B 176 ILE cc_start: 0.7205 (mm) cc_final: 0.6768 (mt) REVERT: B 188 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7913 (m-70) REVERT: B 259 ASP cc_start: 0.7797 (t70) cc_final: 0.7577 (t0) REVERT: B 308 ASP cc_start: 0.7422 (m-30) cc_final: 0.7148 (m-30) REVERT: E 82 MET cc_start: 0.7837 (mmt) cc_final: 0.7195 (mmm) REVERT: E 102 TYR cc_start: 0.7987 (t80) cc_final: 0.7690 (t80) REVERT: E 140 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7282 (mtm) REVERT: E 224 VAL cc_start: 0.8081 (t) cc_final: 0.7843 (p) REVERT: R 108 ASN cc_start: 0.7375 (t0) cc_final: 0.6716 (t0) REVERT: R 137 ASN cc_start: 0.7114 (m-40) cc_final: 0.6877 (m-40) REVERT: R 220 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: R 224 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.5949 (t80) REVERT: R 364 ILE cc_start: 0.5582 (mt) cc_final: 0.5251 (mt) REVERT: R 367 ILE cc_start: 0.6764 (pt) cc_final: 0.6533 (mt) outliers start: 54 outliers final: 46 residues processed: 222 average time/residue: 0.2467 time to fit residues: 71.8785 Evaluate side-chains 241 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128688 restraints weight = 12540.030| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.18 r_work: 0.3593 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9180 Z= 0.190 Angle : 0.605 12.070 12450 Z= 0.306 Chirality : 0.043 0.163 1416 Planarity : 0.004 0.055 1580 Dihedral : 4.186 17.941 1244 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 5.38 % Allowed : 27.20 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1131 helix: 1.36 (0.27), residues: 376 sheet: 0.39 (0.31), residues: 268 loop : -0.88 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.004 0.001 HIS G 44 PHE 0.013 0.001 PHE A 187 TYR 0.019 0.001 TYR E 235 ARG 0.010 0.001 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2741.32 seconds wall clock time: 49 minutes 31.26 seconds (2971.26 seconds total)