Starting phenix.real_space_refine on Fri Nov 15 10:09:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu2_35714/11_2024/8iu2_35714.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu2_35714/11_2024/8iu2_35714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu2_35714/11_2024/8iu2_35714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu2_35714/11_2024/8iu2_35714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu2_35714/11_2024/8iu2_35714.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu2_35714/11_2024/8iu2_35714.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 5591 2.51 5 N 1481 2.21 5 O 1595 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-5513/modules/chem_data/mon_lib" Total number of atoms: 8734 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2338 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 280} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1751 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N TRP R 177 " occ=0.50 ... (12 atoms not shown) pdb=" CH2 TRP R 177 " occ=0.50 residue: pdb=" N PHE R 329 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE R 329 " occ=0.50 Time building chain proxies: 5.89, per 1000 atoms: 0.67 Number of scatterers: 8734 At special positions: 0 Unit cell: (89.512, 123.58, 128.256, 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 1595 8.00 N 1481 7.00 C 5591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 126 " - pdb=" SG CYS R 203 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 36.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'R' and resid 49 through 81 removed outlier: 3.768A pdb=" N TYR R 53 " --> pdb=" O PRO R 49 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 117 removed outlier: 3.525A pdb=" N VAL R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 157 Processing helix chain 'R' and resid 165 through 185 removed outlier: 4.010A pdb=" N ALA R 169 " --> pdb=" O ASP R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 215 through 228 removed outlier: 3.549A pdb=" N ILE R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 253 removed outlier: 3.644A pdb=" N ILE R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 294 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 300 through 323 removed outlier: 3.625A pdb=" N LEU R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) Proline residue: R 307 - end of helix removed outlier: 4.035A pdb=" N THR R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE R 316 " --> pdb=" O LYS R 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 326 through 335 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.581A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.524A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.605A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.570A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.704A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.715A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.632A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.626A pdb=" N SER S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 56' Processing sheet with id=AA1, first strand: chain 'R' and resid 194 through 197 removed outlier: 3.625A pdb=" N HIS R 197 " --> pdb=" O SER R 202 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER R 202 " --> pdb=" O HIS R 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.692A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.593A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.613A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.782A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.613A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.586A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.805A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.478A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.783A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.619A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.747A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.747A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AB7, first strand: chain 'S' and resid 155 through 157 removed outlier: 3.503A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR S 213 " --> pdb=" O SER S 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 177 through 178 402 hydrogen bonds defined for protein. 1158 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: 2.31 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2221 1.33 - 1.45: 1926 1.45 - 1.57: 4697 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8940 Sorted by residual: bond pdb=" N LEU R 306 " pdb=" CA LEU R 306 " ideal model delta sigma weight residual 1.462 1.495 -0.033 9.50e-03 1.11e+04 1.21e+01 bond pdb=" N VAL R 120 " pdb=" CA VAL R 120 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.08e-02 8.57e+03 1.11e+01 bond pdb=" N ASN R 318 " pdb=" CA ASN R 318 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.20e-03 1.18e+04 1.10e+01 bond pdb=" N GLY R 122 " pdb=" CA GLY R 122 " ideal model delta sigma weight residual 1.448 1.477 -0.028 8.80e-03 1.29e+04 1.04e+01 bond pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.12e-02 7.97e+03 9.49e+00 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11559 2.53 - 5.06: 544 5.06 - 7.59: 40 7.59 - 10.12: 7 10.12 - 12.65: 3 Bond angle restraints: 12153 Sorted by residual: angle pdb=" N PRO R 186 " pdb=" CA PRO R 186 " pdb=" C PRO R 186 " ideal model delta sigma weight residual 110.70 119.15 -8.45 1.22e+00 6.72e-01 4.79e+01 angle pdb=" CA GLY R 122 " pdb=" C GLY R 122 " pdb=" O GLY R 122 " ideal model delta sigma weight residual 122.37 118.10 4.27 7.30e-01 1.88e+00 3.43e+01 angle pdb=" N THR A 329 " pdb=" CA THR A 329 " pdb=" C THR A 329 " ideal model delta sigma weight residual 113.02 106.70 6.32 1.20e+00 6.94e-01 2.78e+01 angle pdb=" CA ASP A 309 " pdb=" C ASP A 309 " pdb=" O ASP A 309 " ideal model delta sigma weight residual 121.99 116.44 5.55 1.14e+00 7.69e-01 2.37e+01 angle pdb=" CA PRO R 186 " pdb=" C PRO R 186 " pdb=" N PRO R 187 " ideal model delta sigma weight residual 117.93 123.41 -5.48 1.20e+00 6.94e-01 2.09e+01 ... (remaining 12148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4956 17.23 - 34.45: 209 34.45 - 51.68: 50 51.68 - 68.91: 6 68.91 - 86.14: 4 Dihedral angle restraints: 5225 sinusoidal: 1933 harmonic: 3292 Sorted by residual: dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N PHE A 354 " pdb=" CA PHE A 354 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 862 0.061 - 0.123: 395 0.123 - 0.184: 96 0.184 - 0.245: 17 0.245 - 0.307: 5 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA TRP R 183 " pdb=" N TRP R 183 " pdb=" C TRP R 183 " pdb=" CB TRP R 183 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1372 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " 0.024 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP S 111 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.023 2.00e-02 2.50e+03 2.41e-02 1.01e+01 pdb=" CG PHE B 234 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 278 " 0.015 2.00e-02 2.50e+03 2.08e-02 7.59e+00 pdb=" CG PHE B 278 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 278 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 278 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 278 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 278 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 278 " 0.003 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2674 2.82 - 3.34: 7710 3.34 - 3.86: 13965 3.86 - 4.38: 15709 4.38 - 4.90: 28188 Nonbonded interactions: 68246 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.314 3.040 nonbonded pdb=" O VAL R 104 " pdb=" OG SER R 107 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.345 3.040 nonbonded pdb=" OG SER B 161 " pdb=" N GLY B 162 " model vdw 2.350 3.120 ... (remaining 68241 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=0.50 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: 2.420 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.012 0.076 8940 Z= 0.795 Angle : 1.186 12.651 12153 Z= 0.759 Chirality : 0.072 0.307 1375 Planarity : 0.006 0.068 1532 Dihedral : 10.944 86.136 3102 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer: Outliers : 1.64 % Allowed : 3.27 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1121 helix: 0.28 (0.24), residues: 390 sheet: -3.37 (0.28), residues: 267 loop : -2.67 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP S 111 HIS 0.013 0.003 HIS S 35 PHE 0.055 0.004 PHE B 234 TYR 0.038 0.004 TYR S 227 ARG 0.009 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8695 (m-70) cc_final: 0.8483 (m90) REVERT: R 207 VAL cc_start: 0.8888 (t) cc_final: 0.8677 (m) REVERT: A 24 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7108 (mtm-85) REVERT: A 346 ASN cc_start: 0.8593 (m110) cc_final: 0.8236 (m110) REVERT: B 44 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7257 (pm20) REVERT: B 86 THR cc_start: 0.9245 (p) cc_final: 0.9000 (p) REVERT: B 214 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7428 (mmt180) REVERT: B 215 GLU cc_start: 0.8714 (mp0) cc_final: 0.8507 (mp0) REVERT: B 295 ASN cc_start: 0.8850 (m-40) cc_final: 0.8633 (m-40) REVERT: B 304 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8095 (ptm160) REVERT: G 16 VAL cc_start: 0.8561 (p) cc_final: 0.8311 (m) REVERT: G 17 GLU cc_start: 0.8692 (tp30) cc_final: 0.8474 (tp30) REVERT: G 27 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8235 (mtt90) REVERT: G 47 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8042 (mp0) REVERT: S 65 LYS cc_start: 0.8539 (tttt) cc_final: 0.8103 (tttp) REVERT: S 87 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.7859 (mtm110) REVERT: S 234 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7616 (pt0) REVERT: S 244 LYS cc_start: 0.8170 (tttm) cc_final: 0.7802 (ttmm) outliers start: 15 outliers final: 6 residues processed: 244 average time/residue: 0.2636 time to fit residues: 84.1958 Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 209 SER Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 GLN R 331 ASN B 44 GLN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN B 340 ASN G 5 ASN S 194 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8940 Z= 0.189 Angle : 0.603 8.400 12153 Z= 0.313 Chirality : 0.043 0.156 1375 Planarity : 0.004 0.056 1532 Dihedral : 7.041 80.330 1242 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.62 % Allowed : 10.47 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1121 helix: 1.86 (0.26), residues: 390 sheet: -2.77 (0.29), residues: 257 loop : -2.30 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 152 HIS 0.003 0.001 HIS S 232 PHE 0.014 0.002 PHE B 234 TYR 0.019 0.001 TYR R 194 ARG 0.005 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8629 (m-70) cc_final: 0.8398 (m90) REVERT: R 302 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7454 (mm) REVERT: A 17 LYS cc_start: 0.8649 (mttt) cc_final: 0.8207 (mtpt) REVERT: A 24 ARG cc_start: 0.7216 (mtm110) cc_final: 0.6987 (mtm-85) REVERT: A 256 ASN cc_start: 0.8877 (t0) cc_final: 0.8417 (t0) REVERT: A 332 VAL cc_start: 0.9099 (m) cc_final: 0.8765 (p) REVERT: A 346 ASN cc_start: 0.8558 (m110) cc_final: 0.8196 (m110) REVERT: B 42 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7080 (ttp80) REVERT: B 44 GLN cc_start: 0.7814 (mm110) cc_final: 0.7350 (pm20) REVERT: B 86 THR cc_start: 0.9253 (p) cc_final: 0.9047 (p) REVERT: B 156 GLN cc_start: 0.8048 (mt0) cc_final: 0.7596 (mt0) REVERT: B 215 GLU cc_start: 0.8754 (mp0) cc_final: 0.8444 (mp0) REVERT: G 17 GLU cc_start: 0.8617 (tp30) cc_final: 0.8406 (tp30) REVERT: G 27 ARG cc_start: 0.8514 (mtt90) cc_final: 0.8087 (mtt90) REVERT: G 47 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7973 (mp0) REVERT: S 65 LYS cc_start: 0.8499 (tttt) cc_final: 0.8102 (tttp) REVERT: S 87 ARG cc_start: 0.8071 (ptp-170) cc_final: 0.7823 (mtm110) REVERT: S 234 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7478 (pt0) REVERT: S 244 LYS cc_start: 0.8258 (tttm) cc_final: 0.7862 (ttmm) outliers start: 24 outliers final: 16 residues processed: 204 average time/residue: 0.2483 time to fit residues: 67.3231 Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 0.2980 chunk 34 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 75 GLN B 220 GLN B 259 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8940 Z= 0.163 Angle : 0.550 8.753 12153 Z= 0.284 Chirality : 0.041 0.148 1375 Planarity : 0.004 0.047 1532 Dihedral : 6.207 78.125 1234 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.16 % Allowed : 13.09 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.25), residues: 1121 helix: 2.24 (0.26), residues: 389 sheet: -2.50 (0.28), residues: 267 loop : -2.10 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 51 HIS 0.002 0.001 HIS B 142 PHE 0.015 0.001 PHE S 68 TYR 0.023 0.001 TYR R 118 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: R 45 TYR cc_start: 0.7921 (m-80) cc_final: 0.7586 (m-80) REVERT: R 152 TRP cc_start: 0.8316 (OUTLIER) cc_final: 0.7590 (t-100) REVERT: R 302 LEU cc_start: 0.7821 (pt) cc_final: 0.7456 (mm) REVERT: A 17 LYS cc_start: 0.8629 (mttt) cc_final: 0.8180 (mtpt) REVERT: A 24 ARG cc_start: 0.7197 (mtm110) cc_final: 0.6899 (mtm-85) REVERT: A 256 ASN cc_start: 0.8857 (t0) cc_final: 0.8412 (t0) REVERT: A 332 VAL cc_start: 0.9097 (m) cc_final: 0.8771 (p) REVERT: A 346 ASN cc_start: 0.8559 (m110) cc_final: 0.8192 (m110) REVERT: B 19 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7731 (ttp-170) REVERT: B 42 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7115 (ttp80) REVERT: B 44 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7390 (pm20) REVERT: B 86 THR cc_start: 0.9264 (p) cc_final: 0.8920 (p) REVERT: B 161 SER cc_start: 0.9274 (t) cc_final: 0.8546 (p) REVERT: B 215 GLU cc_start: 0.8827 (mp0) cc_final: 0.8410 (mp0) REVERT: G 27 ARG cc_start: 0.8500 (mtt90) cc_final: 0.8054 (mtt90) REVERT: G 47 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7965 (mp0) REVERT: S 65 LYS cc_start: 0.8598 (tttt) cc_final: 0.8193 (tttp) REVERT: S 95 TYR cc_start: 0.8485 (m-80) cc_final: 0.7525 (m-80) REVERT: S 160 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7672 (ttm-80) REVERT: S 234 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7512 (pt0) REVERT: S 244 LYS cc_start: 0.8302 (tttm) cc_final: 0.7885 (ttmm) outliers start: 29 outliers final: 17 residues processed: 190 average time/residue: 0.2432 time to fit residues: 61.6993 Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 152 TRP Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 11 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.0050 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8940 Z= 0.190 Angle : 0.546 9.781 12153 Z= 0.280 Chirality : 0.041 0.170 1375 Planarity : 0.004 0.045 1532 Dihedral : 6.064 78.661 1234 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.60 % Allowed : 13.85 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.79 (0.25), residues: 1121 helix: 2.41 (0.26), residues: 389 sheet: -2.43 (0.27), residues: 283 loop : -1.87 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 51 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE S 68 TYR 0.023 0.001 TYR R 118 ARG 0.004 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7485 (t-100) REVERT: R 302 LEU cc_start: 0.7769 (pt) cc_final: 0.7407 (mm) REVERT: R 331 ASN cc_start: 0.7790 (p0) cc_final: 0.7367 (p0) REVERT: A 17 LYS cc_start: 0.8614 (mttt) cc_final: 0.8173 (mtpt) REVERT: A 24 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6897 (mtm-85) REVERT: A 256 ASN cc_start: 0.8873 (t0) cc_final: 0.8430 (t0) REVERT: A 332 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8783 (p) REVERT: B 42 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7216 (ttp80) REVERT: B 161 SER cc_start: 0.9298 (t) cc_final: 0.8553 (p) REVERT: G 27 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8218 (mtt90) REVERT: G 47 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7963 (mp0) REVERT: S 65 LYS cc_start: 0.8596 (tttt) cc_final: 0.8183 (tttp) REVERT: S 160 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7139 (mmm-85) REVERT: S 234 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7587 (pt0) REVERT: S 244 LYS cc_start: 0.8319 (tttm) cc_final: 0.7895 (ttmm) outliers start: 33 outliers final: 26 residues processed: 179 average time/residue: 0.2462 time to fit residues: 59.7823 Evaluate side-chains 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 152 TRP Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 0.0000 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 94 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8940 Z= 0.192 Angle : 0.534 10.186 12153 Z= 0.273 Chirality : 0.041 0.140 1375 Planarity : 0.004 0.045 1532 Dihedral : 6.010 78.986 1234 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.25 % Allowed : 14.61 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.65 (0.26), residues: 1121 helix: 2.46 (0.26), residues: 389 sheet: -2.30 (0.27), residues: 285 loop : -1.74 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 152 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE S 68 TYR 0.023 0.001 TYR R 118 ARG 0.003 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 45 TYR cc_start: 0.7145 (m-80) cc_final: 0.6574 (m-80) REVERT: R 50 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7500 (mpp80) REVERT: R 54 HIS cc_start: 0.8630 (m90) cc_final: 0.8291 (m90) REVERT: R 152 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.8062 (t60) REVERT: R 302 LEU cc_start: 0.7768 (pt) cc_final: 0.7399 (mm) REVERT: R 331 ASN cc_start: 0.7812 (p0) cc_final: 0.7398 (p0) REVERT: A 17 LYS cc_start: 0.8621 (mttt) cc_final: 0.8179 (mtpt) REVERT: A 24 ARG cc_start: 0.7238 (mtm110) cc_final: 0.6887 (mtm-85) REVERT: A 256 ASN cc_start: 0.8885 (t0) cc_final: 0.8452 (t0) REVERT: A 332 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8803 (p) REVERT: B 42 ARG cc_start: 0.7535 (ttp80) cc_final: 0.6961 (ttp80) REVERT: B 44 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7423 (pm20) REVERT: B 161 SER cc_start: 0.9287 (t) cc_final: 0.8533 (p) REVERT: G 27 ARG cc_start: 0.8538 (mtt90) cc_final: 0.8232 (mtt90) REVERT: G 47 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7961 (mp0) REVERT: S 65 LYS cc_start: 0.8604 (tttt) cc_final: 0.8197 (tttp) REVERT: S 87 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7825 (ptp-110) REVERT: S 160 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7136 (mmm-85) REVERT: S 234 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7577 (pt0) REVERT: S 244 LYS cc_start: 0.8341 (tttm) cc_final: 0.7901 (ttmm) outliers start: 39 outliers final: 28 residues processed: 193 average time/residue: 0.2462 time to fit residues: 62.6204 Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 152 TRP Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.0270 overall best weight: 2.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 HIS R 217 GLN R 294 ASN B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8940 Z= 0.397 Angle : 0.631 9.710 12153 Z= 0.325 Chirality : 0.044 0.150 1375 Planarity : 0.004 0.050 1532 Dihedral : 6.360 79.373 1234 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.14 % Allowed : 15.05 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.80 (0.25), residues: 1121 helix: 2.31 (0.27), residues: 388 sheet: -2.42 (0.27), residues: 278 loop : -1.80 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 152 HIS 0.006 0.001 HIS B 91 PHE 0.016 0.002 PHE B 235 TYR 0.022 0.002 TYR S 190 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8686 (m90) cc_final: 0.8365 (m90) REVERT: R 302 LEU cc_start: 0.7860 (pt) cc_final: 0.7508 (mm) REVERT: R 331 ASN cc_start: 0.7812 (p0) cc_final: 0.7429 (p0) REVERT: A 17 LYS cc_start: 0.8707 (mttt) cc_final: 0.8262 (mtpt) REVERT: A 24 ARG cc_start: 0.7348 (mtm110) cc_final: 0.6939 (mtm-85) REVERT: A 256 ASN cc_start: 0.8939 (t0) cc_final: 0.8450 (t0) REVERT: B 42 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6978 (ttp80) REVERT: B 44 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7453 (pm20) REVERT: B 262 MET cc_start: 0.8248 (mpp) cc_final: 0.7492 (mpp) REVERT: G 27 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8202 (mtt90) REVERT: G 47 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8032 (mp0) REVERT: S 65 LYS cc_start: 0.8612 (tttt) cc_final: 0.8208 (tttp) REVERT: S 98 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8470 (ptt-90) REVERT: S 160 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7245 (mmm-85) REVERT: S 234 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7613 (pt0) REVERT: S 244 LYS cc_start: 0.8314 (tttm) cc_final: 0.7854 (ttmm) outliers start: 38 outliers final: 31 residues processed: 183 average time/residue: 0.2341 time to fit residues: 57.3700 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 278 CYS Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8940 Z= 0.154 Angle : 0.538 11.447 12153 Z= 0.275 Chirality : 0.041 0.153 1375 Planarity : 0.004 0.047 1532 Dihedral : 6.069 81.348 1234 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.05 % Allowed : 16.25 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.58 (0.26), residues: 1121 helix: 2.45 (0.27), residues: 387 sheet: -2.23 (0.28), residues: 284 loop : -1.65 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 142 HIS 0.002 0.001 HIS S 232 PHE 0.020 0.001 PHE S 68 TYR 0.026 0.001 TYR R 118 ARG 0.004 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8670 (m90) cc_final: 0.8326 (m90) REVERT: R 302 LEU cc_start: 0.7813 (pt) cc_final: 0.7464 (mm) REVERT: R 331 ASN cc_start: 0.7838 (p0) cc_final: 0.7448 (p0) REVERT: A 17 LYS cc_start: 0.8616 (mttt) cc_final: 0.8177 (mtpt) REVERT: A 24 ARG cc_start: 0.7262 (mtm110) cc_final: 0.6886 (mtm-85) REVERT: A 256 ASN cc_start: 0.8903 (t0) cc_final: 0.8505 (t0) REVERT: B 42 ARG cc_start: 0.7598 (ttp80) cc_final: 0.6964 (ttp80) REVERT: B 44 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7469 (pm20) REVERT: B 161 SER cc_start: 0.9319 (t) cc_final: 0.8561 (p) REVERT: B 262 MET cc_start: 0.8163 (mpp) cc_final: 0.7494 (mpp) REVERT: G 27 ARG cc_start: 0.8538 (mtt90) cc_final: 0.8230 (mtt90) REVERT: G 47 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7963 (mp0) REVERT: S 65 LYS cc_start: 0.8712 (tttt) cc_final: 0.8316 (tttp) REVERT: S 98 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8462 (ptt-90) REVERT: S 160 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7155 (mmm-85) REVERT: S 234 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7555 (pt0) REVERT: S 244 LYS cc_start: 0.8311 (tttm) cc_final: 0.7861 (ttmm) outliers start: 28 outliers final: 21 residues processed: 183 average time/residue: 0.2304 time to fit residues: 56.6567 Evaluate side-chains 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 278 CYS Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.0570 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 GLN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8940 Z= 0.168 Angle : 0.553 11.549 12153 Z= 0.277 Chirality : 0.041 0.151 1375 Planarity : 0.004 0.045 1532 Dihedral : 5.982 82.827 1234 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.16 % Allowed : 16.47 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.26), residues: 1121 helix: 2.52 (0.27), residues: 386 sheet: -2.05 (0.28), residues: 278 loop : -1.56 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 142 HIS 0.002 0.001 HIS A 188 PHE 0.016 0.001 PHE S 68 TYR 0.023 0.001 TYR R 118 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8659 (m90) cc_final: 0.8367 (m-70) REVERT: R 302 LEU cc_start: 0.7776 (pt) cc_final: 0.7423 (mm) REVERT: R 331 ASN cc_start: 0.7831 (p0) cc_final: 0.7446 (p0) REVERT: A 17 LYS cc_start: 0.8594 (mttt) cc_final: 0.8171 (mtpt) REVERT: A 24 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6892 (mtm-85) REVERT: A 256 ASN cc_start: 0.8905 (t0) cc_final: 0.8518 (t0) REVERT: B 42 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7000 (ttp80) REVERT: B 44 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7453 (pm20) REVERT: B 161 SER cc_start: 0.9287 (t) cc_final: 0.8508 (p) REVERT: B 262 MET cc_start: 0.8170 (mpp) cc_final: 0.7512 (mpp) REVERT: G 27 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8222 (mtt90) REVERT: G 47 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7891 (mp0) REVERT: S 65 LYS cc_start: 0.8699 (tttt) cc_final: 0.8280 (tttp) REVERT: S 98 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8573 (ptt-90) REVERT: S 160 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7194 (mmm-85) REVERT: S 234 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7576 (pt0) REVERT: S 244 LYS cc_start: 0.8307 (tttm) cc_final: 0.7860 (ttmm) outliers start: 29 outliers final: 25 residues processed: 183 average time/residue: 0.2305 time to fit residues: 56.7872 Evaluate side-chains 180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 278 CYS Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8940 Z= 0.163 Angle : 0.545 12.384 12153 Z= 0.274 Chirality : 0.041 0.149 1375 Planarity : 0.004 0.044 1532 Dihedral : 5.923 84.261 1234 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.38 % Allowed : 16.47 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.26), residues: 1121 helix: 2.59 (0.27), residues: 386 sheet: -1.91 (0.28), residues: 280 loop : -1.48 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 142 HIS 0.002 0.000 HIS B 142 PHE 0.024 0.001 PHE S 68 TYR 0.024 0.001 TYR R 118 ARG 0.002 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8655 (m90) cc_final: 0.8359 (m-70) REVERT: R 302 LEU cc_start: 0.7815 (pt) cc_final: 0.7466 (mm) REVERT: R 331 ASN cc_start: 0.7822 (p0) cc_final: 0.7440 (p0) REVERT: A 17 LYS cc_start: 0.8544 (mttt) cc_final: 0.8142 (mtpt) REVERT: A 24 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6889 (mtm-85) REVERT: A 256 ASN cc_start: 0.8906 (t0) cc_final: 0.8539 (t0) REVERT: B 42 ARG cc_start: 0.7541 (ttp80) cc_final: 0.6963 (ttp80) REVERT: B 44 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7458 (pm20) REVERT: B 161 SER cc_start: 0.9249 (t) cc_final: 0.8487 (p) REVERT: B 215 GLU cc_start: 0.8687 (mp0) cc_final: 0.8420 (mp0) REVERT: B 262 MET cc_start: 0.8075 (mpp) cc_final: 0.7549 (mpp) REVERT: G 27 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8227 (mtt90) REVERT: G 47 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7844 (mp0) REVERT: S 65 LYS cc_start: 0.8750 (tttt) cc_final: 0.8333 (tttp) REVERT: S 77 ASN cc_start: 0.8268 (m-40) cc_final: 0.7400 (t0) REVERT: S 98 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8433 (ptt-90) REVERT: S 160 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7178 (mmm-85) REVERT: S 234 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7557 (pt0) REVERT: S 244 LYS cc_start: 0.8297 (tttm) cc_final: 0.7847 (ttmm) outliers start: 31 outliers final: 25 residues processed: 180 average time/residue: 0.2346 time to fit residues: 57.0758 Evaluate side-chains 173 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 278 CYS Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8940 Z= 0.233 Angle : 0.570 12.060 12153 Z= 0.287 Chirality : 0.042 0.146 1375 Planarity : 0.004 0.045 1532 Dihedral : 5.979 79.641 1234 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.05 % Allowed : 17.34 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.34 (0.26), residues: 1121 helix: 2.52 (0.27), residues: 389 sheet: -1.98 (0.28), residues: 280 loop : -1.50 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 36 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE S 68 TYR 0.023 0.001 TYR R 118 ARG 0.002 0.000 ARG S 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8676 (m90) cc_final: 0.8367 (m-70) REVERT: R 302 LEU cc_start: 0.7894 (pt) cc_final: 0.7564 (mm) REVERT: R 331 ASN cc_start: 0.7811 (p0) cc_final: 0.7430 (p0) REVERT: A 17 LYS cc_start: 0.8578 (mttt) cc_final: 0.8168 (mtpt) REVERT: A 24 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6920 (mtm-85) REVERT: A 256 ASN cc_start: 0.8920 (t0) cc_final: 0.8559 (t0) REVERT: B 42 ARG cc_start: 0.7571 (ttp80) cc_final: 0.6987 (ttp80) REVERT: B 44 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7475 (pm20) REVERT: B 161 SER cc_start: 0.9329 (t) cc_final: 0.8569 (p) REVERT: B 215 GLU cc_start: 0.8674 (mp0) cc_final: 0.8382 (mp0) REVERT: B 262 MET cc_start: 0.8056 (mpp) cc_final: 0.7611 (mpp) REVERT: G 27 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8256 (mtt90) REVERT: G 47 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7826 (mp0) REVERT: S 65 LYS cc_start: 0.8759 (tttt) cc_final: 0.8338 (tttp) REVERT: S 77 ASN cc_start: 0.8307 (m-40) cc_final: 0.7582 (t0) REVERT: S 98 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8524 (ptt-90) REVERT: S 160 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7213 (mmm-85) REVERT: S 234 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7604 (pt0) REVERT: S 244 LYS cc_start: 0.8287 (tttm) cc_final: 0.7855 (ttmm) outliers start: 28 outliers final: 24 residues processed: 172 average time/residue: 0.2418 time to fit residues: 55.6681 Evaluate side-chains 173 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.0270 chunk 63 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093553 restraints weight = 14114.970| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.89 r_work: 0.3062 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8940 Z= 0.164 Angle : 0.548 12.658 12153 Z= 0.275 Chirality : 0.041 0.148 1375 Planarity : 0.004 0.044 1532 Dihedral : 5.890 80.395 1234 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.73 % Allowed : 17.88 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.26), residues: 1121 helix: 2.61 (0.27), residues: 386 sheet: -1.80 (0.29), residues: 277 loop : -1.39 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 142 HIS 0.002 0.000 HIS B 91 PHE 0.016 0.001 PHE S 68 TYR 0.027 0.001 TYR R 118 ARG 0.002 0.000 ARG S 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.38 seconds wall clock time: 42 minutes 25.95 seconds (2545.95 seconds total)