Starting phenix.real_space_refine on Sat Apr 6 01:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/04_2024/8unw_42419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/04_2024/8unw_42419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/04_2024/8unw_42419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/04_2024/8unw_42419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/04_2024/8unw_42419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/04_2024/8unw_42419_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 41 5.16 5 C 4277 2.51 5 N 1146 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 138": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6647 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1711 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1699 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 146 Conformer: "B" Number of residues, atoms: 231, 1699 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 146 bond proxies already assigned to first conformer: 1718 Chain: "B" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2403 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 122 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 352 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2133 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.00, per 1000 atoms: 0.75 Number of scatterers: 6647 At special positions: 0 Unit cell: (82.4315, 131.89, 99.7855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 3 15.00 O 1180 8.00 N 1146 7.00 C 4277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 8 sheets defined 42.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 4.066A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.520A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.637A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 36 through 60 removed outlier: 3.580A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.523A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.935A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 163 removed outlier: 3.808A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.557A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 237 removed outlier: 3.706A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 286 removed outlier: 4.048A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 298 removed outlier: 4.695A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.535A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.063A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.761A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.080A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.818A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 265 removed outlier: 3.838A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.735A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.738A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 942 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: 1.81 Time building geometry restraints manager: 2.80 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: 1598 1.33 - 1.45: 1418 1.45 - 1.57: 3714 1.57 - 1.69: 5 1.69 - 1.81: 56 Bond restraints: 6791 Sorted by residual: bond pdb=" C ARG A 231 " pdb=" N ARG A 232 " ideal model delta sigma weight residual 1.331 1.393 -0.063 1.66e-02 3.63e+03 1.43e+01 bond pdb=" C ARG A 232 " pdb=" N LYS A 233 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.49e-02 4.50e+03 1.25e+01 bond pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N VAL A 301 " pdb=" CA VAL A 301 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.40e+00 bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.36e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 174 107.06 - 113.80: 3822 113.80 - 120.54: 2720 120.54 - 127.28: 2492 127.28 - 134.02: 75 Bond angle restraints: 9283 Sorted by residual: angle pdb=" N LEU G 19 " pdb=" CA LEU G 19 " pdb=" C LEU G 19 " ideal model delta sigma weight residual 111.71 103.18 8.53 1.15e+00 7.56e-01 5.50e+01 angle pdb=" N LEU G 15 " pdb=" CA LEU G 15 " pdb=" C LEU G 15 " ideal model delta sigma weight residual 111.28 104.28 7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" N TYR A 253 " pdb=" CA TYR A 253 " pdb=" C TYR A 253 " ideal model delta sigma weight residual 113.72 105.47 8.25 1.30e+00 5.92e-01 4.03e+01 angle pdb=" N ASN A 264 " pdb=" CA ASN A 264 " pdb=" C ASN A 264 " ideal model delta sigma weight residual 110.35 101.86 8.49 1.36e+00 5.41e-01 3.90e+01 angle pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sigma weight residual 113.80 119.12 -5.32 1.00e+00 1.00e+00 2.83e+01 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 3867 35.25 - 70.51: 55 70.51 - 105.76: 1 105.76 - 141.02: 0 141.02 - 176.27: 5 Dihedral angle restraints: 3928 sinusoidal: 1298 harmonic: 2630 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 127.52 176.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 15.15 162.15 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -57.10 161.70 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 3925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 851 0.056 - 0.111: 190 0.111 - 0.166: 45 0.166 - 0.222: 19 0.222 - 0.277: 4 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA LEU G 15 " pdb=" N LEU G 15 " pdb=" C LEU G 15 " pdb=" CB LEU G 15 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ARG A 231 " pdb=" N ARG A 231 " pdb=" C ARG A 231 " pdb=" CB ARG A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1106 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 348 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C ILE A 348 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 348 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 349 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 212 " 0.011 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C ASP B 212 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP B 212 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 213 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 18 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C GLN G 18 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN G 18 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU G 19 " -0.013 2.00e-02 2.50e+03 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 797 2.75 - 3.29: 6365 3.29 - 3.83: 10450 3.83 - 4.36: 11480 4.36 - 4.90: 21102 Nonbonded interactions: 50194 Sorted by model distance: nonbonded pdb=" O ASN A 264 " pdb=" OD1 ASN A 264 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR R 219 " pdb=" O HOH R 601 " model vdw 2.268 2.440 nonbonded pdb=" O THR A 55 " pdb=" N LYS A 58 " model vdw 2.344 2.520 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.349 2.440 ... (remaining 50189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 1.660 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: 7.690 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.910 Find NCS groups from input model: 0.170 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.005 0.063 6791 Z= 0.355 Angle : 0.917 11.708 9283 Z= 0.622 Chirality : 0.056 0.277 1109 Planarity : 0.004 0.059 1157 Dihedral : 15.253 176.272 2214 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % 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: 0.86 (0.29), residues: 885 helix: 2.13 (0.28), residues: 378 sheet: -0.07 (0.40), residues: 179 loop : -0.90 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.022 0.001 PHE A 212 TYR 0.017 0.001 TYR R 308 ARG 0.005 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.638 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1851 time to fit residues: 28.7525 Evaluate side-chains 91 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN R 196 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6791 Z= 0.169 Angle : 0.485 7.253 9283 Z= 0.260 Chirality : 0.040 0.135 1109 Planarity : 0.003 0.039 1157 Dihedral : 11.402 164.243 989 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.94 % Allowed : 7.94 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 885 helix: 2.25 (0.28), residues: 382 sheet: 0.05 (0.41), residues: 176 loop : -0.82 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR R 316 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.768 Fit side-chains REVERT: B 260 GLU cc_start: 0.8512 (pt0) cc_final: 0.8300 (pt0) REVERT: G 18 GLN cc_start: 0.8270 (tp40) cc_final: 0.8003 (tp40) REVERT: R 61 PHE cc_start: 0.7214 (m-10) cc_final: 0.6772 (m-10) REVERT: R 82 MET cc_start: 0.7495 (ttt) cc_final: 0.7226 (ttt) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.1738 time to fit residues: 25.5535 Evaluate side-chains 105 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6791 Z= 0.195 Angle : 0.475 6.929 9283 Z= 0.254 Chirality : 0.040 0.131 1109 Planarity : 0.003 0.041 1157 Dihedral : 11.001 160.223 989 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.11 % Allowed : 11.35 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 885 helix: 2.33 (0.28), residues: 382 sheet: -0.02 (0.41), residues: 176 loop : -0.83 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.016 0.001 TYR B 111 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.690 Fit side-chains REVERT: B 59 TYR cc_start: 0.8599 (m-10) cc_final: 0.8238 (m-10) REVERT: R 61 PHE cc_start: 0.7261 (m-10) cc_final: 0.6797 (m-10) REVERT: R 82 MET cc_start: 0.7557 (ttt) cc_final: 0.7248 (ttp) outliers start: 13 outliers final: 12 residues processed: 105 average time/residue: 0.1769 time to fit residues: 25.7253 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6791 Z= 0.175 Angle : 0.459 6.496 9283 Z= 0.245 Chirality : 0.040 0.129 1109 Planarity : 0.003 0.041 1157 Dihedral : 10.552 162.705 989 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.27 % Allowed : 13.61 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 885 helix: 2.26 (0.28), residues: 385 sheet: -0.07 (0.40), residues: 176 loop : -0.77 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.008 0.001 TYR R 316 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.768 Fit side-chains REVERT: B 59 TYR cc_start: 0.8573 (m-10) cc_final: 0.8291 (m-10) REVERT: R 82 MET cc_start: 0.7567 (ttt) cc_final: 0.7235 (ttp) outliers start: 14 outliers final: 14 residues processed: 100 average time/residue: 0.1732 time to fit residues: 23.9161 Evaluate side-chains 99 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 239 ASN R 196 ASN R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6791 Z= 0.290 Angle : 0.506 6.585 9283 Z= 0.273 Chirality : 0.041 0.128 1109 Planarity : 0.003 0.046 1157 Dihedral : 10.129 165.048 989 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.24 % Allowed : 13.94 % Favored : 82.82 % 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: 0.91 (0.29), residues: 885 helix: 2.13 (0.28), residues: 384 sheet: -0.14 (0.41), residues: 171 loop : -0.81 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE B 241 TYR 0.010 0.001 TYR R 316 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.685 Fit side-chains REVERT: R 82 MET cc_start: 0.7644 (ttt) cc_final: 0.7328 (ttp) REVERT: R 231 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8115 (tm-30) outliers start: 20 outliers final: 18 residues processed: 105 average time/residue: 0.1694 time to fit residues: 24.3425 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 83 optimal weight: 0.0270 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS R 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6791 Z= 0.138 Angle : 0.446 6.446 9283 Z= 0.238 Chirality : 0.039 0.127 1109 Planarity : 0.003 0.041 1157 Dihedral : 9.486 169.852 989 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.11 % Allowed : 16.53 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 885 helix: 2.24 (0.28), residues: 384 sheet: -0.14 (0.40), residues: 176 loop : -0.77 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.010 0.001 PHE A 212 TYR 0.008 0.001 TYR R 316 ARG 0.004 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.780 Fit side-chains REVERT: R 61 PHE cc_start: 0.6991 (m-10) cc_final: 0.6677 (m-10) REVERT: R 82 MET cc_start: 0.7533 (ttt) cc_final: 0.7121 (ttp) REVERT: R 231 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8042 (tm-30) outliers start: 13 outliers final: 11 residues processed: 104 average time/residue: 0.1733 time to fit residues: 24.7276 Evaluate side-chains 97 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 85 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6791 Z= 0.136 Angle : 0.441 6.411 9283 Z= 0.234 Chirality : 0.039 0.125 1109 Planarity : 0.003 0.041 1157 Dihedral : 9.051 172.581 989 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.11 % Allowed : 16.53 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 885 helix: 2.25 (0.28), residues: 384 sheet: -0.09 (0.40), residues: 176 loop : -0.72 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR R 316 ARG 0.004 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.790 Fit side-chains REVERT: R 61 PHE cc_start: 0.6882 (m-10) cc_final: 0.6564 (m-10) REVERT: R 82 MET cc_start: 0.7498 (ttt) cc_final: 0.7152 (ttp) REVERT: R 231 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8031 (tm-30) outliers start: 13 outliers final: 13 residues processed: 100 average time/residue: 0.1791 time to fit residues: 24.7175 Evaluate side-chains 99 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6791 Z= 0.325 Angle : 0.528 6.685 9283 Z= 0.283 Chirality : 0.042 0.145 1109 Planarity : 0.004 0.047 1157 Dihedral : 8.810 171.480 989 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.08 % Allowed : 15.72 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 885 helix: 2.05 (0.28), residues: 385 sheet: -0.14 (0.41), residues: 171 loop : -0.80 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.009 0.001 HIS A 220 PHE 0.019 0.002 PHE B 241 TYR 0.010 0.001 TYR A 339 ARG 0.004 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.727 Fit side-chains REVERT: R 61 PHE cc_start: 0.7112 (m-10) cc_final: 0.6772 (m-10) REVERT: R 82 MET cc_start: 0.7635 (ttt) cc_final: 0.7336 (ttp) outliers start: 19 outliers final: 18 residues processed: 99 average time/residue: 0.1696 time to fit residues: 23.2923 Evaluate side-chains 103 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 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 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6791 Z= 0.150 Angle : 0.457 6.782 9283 Z= 0.243 Chirality : 0.040 0.126 1109 Planarity : 0.003 0.042 1157 Dihedral : 8.475 169.348 989 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.59 % Allowed : 16.21 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 885 helix: 2.12 (0.28), residues: 385 sheet: -0.19 (0.41), residues: 176 loop : -0.67 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR R 316 ARG 0.006 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.714 Fit side-chains REVERT: R 61 PHE cc_start: 0.6960 (m-10) cc_final: 0.6667 (m-10) REVERT: R 82 MET cc_start: 0.7519 (ttt) cc_final: 0.7212 (ttp) outliers start: 16 outliers final: 15 residues processed: 99 average time/residue: 0.1789 time to fit residues: 24.0992 Evaluate side-chains 100 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8188 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6791 Z= 0.153 Angle : 0.461 6.760 9283 Z= 0.246 Chirality : 0.040 0.152 1109 Planarity : 0.003 0.043 1157 Dihedral : 8.298 165.540 989 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.59 % Allowed : 16.37 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 885 helix: 2.18 (0.28), residues: 384 sheet: -0.15 (0.41), residues: 178 loop : -0.60 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR R 316 ARG 0.006 0.000 ARG R 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.756 Fit side-chains REVERT: A 343 ASP cc_start: 0.8085 (m-30) cc_final: 0.7787 (m-30) REVERT: B 59 TYR cc_start: 0.8589 (m-10) cc_final: 0.8098 (m-10) REVERT: R 61 PHE cc_start: 0.6924 (m-10) cc_final: 0.6614 (m-10) REVERT: R 82 MET cc_start: 0.7512 (ttt) cc_final: 0.7170 (ttp) outliers start: 16 outliers final: 15 residues processed: 99 average time/residue: 0.1741 time to fit residues: 23.9436 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 196 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099132 restraints weight = 47045.764| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 6.19 r_work: 0.2980 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6791 Z= 0.137 Angle : 0.452 6.719 9283 Z= 0.242 Chirality : 0.039 0.154 1109 Planarity : 0.003 0.055 1157 Dihedral : 8.039 160.045 989 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.59 % Allowed : 16.69 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.29), residues: 885 helix: 2.25 (0.28), residues: 383 sheet: -0.09 (0.41), residues: 176 loop : -0.65 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR R 316 ARG 0.006 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.96 seconds wall clock time: 31 minutes 34.98 seconds (1894.98 seconds total)