Starting phenix.real_space_refine on Thu Feb 13 14:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oij_20078/02_2025/6oij_20078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oij_20078/02_2025/6oij_20078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oij_20078/02_2025/6oij_20078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oij_20078/02_2025/6oij_20078.map" model { file = "/net/cci-nas-00/data/ceres_data/6oij_20078/02_2025/6oij_20078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oij_20078/02_2025/6oij_20078.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5697 2.51 5 N 1500 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8877 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1781 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2273 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1757 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'IXO': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.20, per 1000 atoms: 0.59 Number of scatterers: 8877 At special positions: 0 Unit cell: (106, 117.66, 107.06, 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 59 16.00 O 1621 8.00 N 1500 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 37 removed outlier: 3.835A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.072A pdb=" N TRP A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.573A pdb=" N GLU A 221 " --> pdb=" O HIS A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 336 through 356 Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.852A pdb=" N TYR R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 89 removed outlier: 3.543A pdb=" N MET R 88 " --> pdb=" O THR R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 168 removed outlier: 4.011A pdb=" N SER R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Proline residue: R 159 - end of helix removed outlier: 3.508A pdb=" N LEU R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.126A pdb=" N LEU R 183 " --> pdb=" O ILE R 180 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER R 184 " --> pdb=" O GLN R 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 180 through 184' Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.577A pdb=" N THR R 189 " --> pdb=" O GLN R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 226 removed outlier: 4.413A pdb=" N ARG R 220 " --> pdb=" O GLU R 216 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU R 221 " --> pdb=" O ASN R 217 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 389 removed outlier: 3.910A pdb=" N ARG R 365 " --> pdb=" O LYS R 361 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 397 through 414 removed outlier: 4.258A pdb=" N CYS R 407 " --> pdb=" O GLY R 403 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR R 408 " --> pdb=" O TYR R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 419 removed outlier: 3.799A pdb=" N TYR R 418 " --> pdb=" O ASN R 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 432 Processing helix chain 'R' and resid 438 through 442 removed outlier: 3.542A pdb=" N TRP R 442 " --> pdb=" O LYS R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 22 removed outlier: 4.391A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 5.871A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 229 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.850A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.790A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.883A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.276A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.718A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.525A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.984A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.640A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1299 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: 2.76 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.44: 2541 1.44 - 1.56: 5037 1.56 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 9074 Sorted by residual: bond pdb=" C GLU H 234 " pdb=" N TYR H 235 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.46e+01 bond pdb=" N11 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.385 1.425 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.310 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C ASP H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.61e+00 bond pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.50e+00 ... (remaining 9069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11965 2.30 - 4.59: 328 4.59 - 6.89: 33 6.89 - 9.19: 12 9.19 - 11.48: 10 Bond angle restraints: 12348 Sorted by residual: angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 122.61 129.80 -7.19 1.56e+00 4.11e-01 2.13e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 108.34 113.73 -5.39 1.31e+00 5.83e-01 1.69e+01 angle pdb=" C TYR R 82 " pdb=" N THR R 83 " pdb=" CA THR R 83 " ideal model delta sigma weight residual 121.14 114.52 6.62 1.75e+00 3.27e-01 1.43e+01 angle pdb=" CA MET H 192 " pdb=" CB MET H 192 " pdb=" CG MET H 192 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N THR R 379 " pdb=" CA THR R 379 " pdb=" C THR R 379 " ideal model delta sigma weight residual 109.81 117.17 -7.36 2.21e+00 2.05e-01 1.11e+01 ... (remaining 12343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 5080 24.20 - 48.40: 302 48.40 - 72.61: 35 72.61 - 96.81: 6 96.81 - 121.01: 4 Dihedral angle restraints: 5427 sinusoidal: 2083 harmonic: 3344 Sorted by residual: dihedral pdb=" CA GLU A 234 " pdb=" C GLU A 234 " pdb=" N TYR A 235 " pdb=" CA TYR A 235 " ideal model delta harmonic sigma weight residual 180.00 149.44 30.56 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 888 0.044 - 0.089: 368 0.089 - 0.133: 136 0.133 - 0.178: 24 0.178 - 0.222: 8 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE R 180 " pdb=" CA ILE R 180 " pdb=" CG1 ILE R 180 " pdb=" CG2 ILE R 180 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE A 200 " pdb=" CA ILE A 200 " pdb=" CG1 ILE A 200 " pdb=" CG2 ILE A 200 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1421 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 236 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 414 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO R 415 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 83 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C THR R 83 " -0.041 2.00e-02 2.50e+03 pdb=" O THR R 83 " 0.015 2.00e-02 2.50e+03 pdb=" N THR R 84 " 0.014 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1689 2.77 - 3.30: 7932 3.30 - 3.83: 14902 3.83 - 4.37: 16879 4.37 - 4.90: 30037 Nonbonded interactions: 71439 Sorted by model distance: nonbonded pdb=" OG1 THR R 377 " pdb=" O LEU R 406 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.266 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.280 3.040 nonbonded pdb=" O LEU R 81 " pdb=" OG1 THR R 84 " model vdw 2.287 3.040 ... (remaining 71434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.006 0.079 9074 Z= 0.397 Angle : 0.942 11.484 12348 Z= 0.500 Chirality : 0.057 0.222 1424 Planarity : 0.007 0.082 1540 Dihedral : 15.714 121.011 3262 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.77 % Allowed : 12.72 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.70 (0.20), residues: 1134 helix: -2.41 (0.19), residues: 395 sheet: -1.87 (0.30), residues: 238 loop : -2.67 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 91 HIS 0.007 0.002 HIS H 35 PHE 0.022 0.002 PHE R 182 TYR 0.018 0.002 TYR R 404 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8503 (tptp) cc_final: 0.7979 (ttpt) REVERT: A 357 ASN cc_start: 0.8445 (t0) cc_final: 0.7799 (t0) REVERT: R 404 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6507 (m-10) REVERT: H 5 VAL cc_start: 0.8470 (m) cc_final: 0.8194 (t) REVERT: H 148 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8032 (Cg_exo) REVERT: H 192 MET cc_start: 0.8501 (ppp) cc_final: 0.8206 (ppp) REVERT: H 246 GLU cc_start: 0.7377 (mp0) cc_final: 0.7048 (mp0) REVERT: G 48 ASP cc_start: 0.8329 (t0) cc_final: 0.8097 (t0) outliers start: 7 outliers final: 2 residues processed: 214 average time/residue: 0.2274 time to fit residues: 65.7840 Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 265 GLN A 274 ASN A 287 HIS R 43 ASN R 61 ASN R 90 HIS R 410 ASN H 142 GLN H 183 GLN B 75 GLN B 88 ASN B 239 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105073 restraints weight = 13305.840| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.24 r_work: 0.3121 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9074 Z= 0.207 Angle : 0.660 9.028 12348 Z= 0.339 Chirality : 0.044 0.271 1424 Planarity : 0.005 0.066 1540 Dihedral : 8.625 73.379 1403 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.99 % Allowed : 17.48 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.23), residues: 1134 helix: -0.35 (0.24), residues: 394 sheet: -1.40 (0.31), residues: 244 loop : -2.23 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 PHE 0.016 0.001 PHE A 55 TYR 0.018 0.001 TYR R 85 ARG 0.003 0.000 ARG R 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.962 Fit side-chains REVERT: A 294 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7092 (pm20) REVERT: A 311 LYS cc_start: 0.8713 (tptp) cc_final: 0.8168 (ttpt) REVERT: A 357 ASN cc_start: 0.8808 (t0) cc_final: 0.8153 (t0) REVERT: R 23 TRP cc_start: 0.7271 (p-90) cc_final: 0.7006 (p-90) REVERT: R 217 ASN cc_start: 0.8502 (t0) cc_final: 0.8146 (t0) REVERT: R 404 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: H 11 LEU cc_start: 0.7776 (tp) cc_final: 0.7379 (mp) REVERT: H 18 ARG cc_start: 0.7275 (tpp80) cc_final: 0.6983 (tpt-90) REVERT: H 148 PRO cc_start: 0.8619 (Cg_endo) cc_final: 0.8235 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7244 (mp0) cc_final: 0.6976 (mp0) REVERT: B 19 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7750 (ttp80) REVERT: G 11 GLN cc_start: 0.8261 (pm20) cc_final: 0.7983 (pm20) outliers start: 27 outliers final: 16 residues processed: 195 average time/residue: 0.2012 time to fit residues: 55.0578 Evaluate side-chains 169 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 ASN H 142 GLN H 167 HIS H 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105172 restraints weight = 13577.256| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.28 r_work: 0.3117 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9074 Z= 0.208 Angle : 0.659 9.028 12348 Z= 0.339 Chirality : 0.044 0.271 1424 Planarity : 0.005 0.067 1540 Dihedral : 8.625 73.379 1403 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.88 % Allowed : 20.13 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.23), residues: 1134 helix: -0.35 (0.24), residues: 394 sheet: -1.40 (0.31), residues: 244 loop : -2.23 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 PHE 0.016 0.001 PHE A 55 TYR 0.018 0.001 TYR R 85 ARG 0.003 0.000 ARG R 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7129 (pm20) REVERT: A 311 LYS cc_start: 0.8742 (tptp) cc_final: 0.8192 (ttpt) REVERT: A 357 ASN cc_start: 0.8805 (t0) cc_final: 0.8159 (t0) REVERT: R 23 TRP cc_start: 0.7267 (p-90) cc_final: 0.7004 (p-90) REVERT: R 217 ASN cc_start: 0.8522 (t0) cc_final: 0.8157 (t0) REVERT: R 404 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: H 11 LEU cc_start: 0.7758 (tp) cc_final: 0.7374 (mp) REVERT: H 18 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6998 (tpt-90) REVERT: H 148 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8243 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7239 (mp0) cc_final: 0.6998 (mp0) REVERT: B 19 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7765 (ttp80) outliers start: 17 outliers final: 16 residues processed: 168 average time/residue: 0.2086 time to fit residues: 48.7242 Evaluate side-chains 167 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 64 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104719 restraints weight = 13416.911| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.25 r_work: 0.3115 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9074 Z= 0.210 Angle : 0.661 9.032 12348 Z= 0.339 Chirality : 0.044 0.270 1424 Planarity : 0.005 0.067 1540 Dihedral : 8.776 73.385 1403 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.88 % Allowed : 20.13 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.23), residues: 1134 helix: -0.34 (0.24), residues: 394 sheet: -1.40 (0.31), residues: 244 loop : -2.23 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS H 167 PHE 0.016 0.001 PHE A 55 TYR 0.017 0.001 TYR R 85 ARG 0.003 0.000 ARG R 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7112 (pm20) REVERT: A 311 LYS cc_start: 0.8735 (tptp) cc_final: 0.8169 (ttpt) REVERT: A 357 ASN cc_start: 0.8817 (t0) cc_final: 0.8156 (t0) REVERT: R 23 TRP cc_start: 0.7272 (p-90) cc_final: 0.7005 (p-90) REVERT: R 217 ASN cc_start: 0.8516 (t0) cc_final: 0.8154 (t0) REVERT: R 404 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: H 11 LEU cc_start: 0.7767 (tp) cc_final: 0.7379 (mp) REVERT: H 18 ARG cc_start: 0.7293 (tpp80) cc_final: 0.6995 (tpt-90) REVERT: H 148 PRO cc_start: 0.8604 (Cg_endo) cc_final: 0.8228 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7232 (mp0) cc_final: 0.6972 (mp0) REVERT: B 19 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7751 (ttp80) outliers start: 17 outliers final: 16 residues processed: 166 average time/residue: 0.2067 time to fit residues: 47.7385 Evaluate side-chains 167 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS R 410 ASN H 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102687 restraints weight = 13440.975| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.22 r_work: 0.3080 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9074 Z= 0.308 Angle : 0.681 11.019 12348 Z= 0.350 Chirality : 0.046 0.192 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.855 79.376 1403 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.32 % Allowed : 19.69 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.46 (0.24), residues: 1134 helix: 0.43 (0.25), residues: 394 sheet: -1.25 (0.32), residues: 248 loop : -1.96 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS A 287 PHE 0.014 0.002 PHE A 341 TYR 0.018 0.002 TYR R 212 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.993 Fit side-chains REVERT: A 271 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8518 (tt) REVERT: A 294 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7111 (pm20) REVERT: A 311 LYS cc_start: 0.8847 (tptp) cc_final: 0.8109 (ttpt) REVERT: R 23 TRP cc_start: 0.7263 (p-90) cc_final: 0.6896 (p-90) REVERT: R 217 ASN cc_start: 0.8429 (t0) cc_final: 0.8088 (t0) REVERT: H 11 LEU cc_start: 0.7734 (tp) cc_final: 0.7425 (mp) REVERT: H 18 ARG cc_start: 0.7301 (tpp80) cc_final: 0.7032 (tpt-90) REVERT: H 148 PRO cc_start: 0.8590 (Cg_endo) cc_final: 0.8198 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7270 (mp0) cc_final: 0.7015 (mp0) REVERT: G 21 MET cc_start: 0.8827 (tpp) cc_final: 0.8567 (tpp) REVERT: G 48 ASP cc_start: 0.8451 (t0) cc_final: 0.8227 (t0) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.2127 time to fit residues: 53.7661 Evaluate side-chains 170 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102885 restraints weight = 13489.876| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.27 r_work: 0.3075 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9074 Z= 0.308 Angle : 0.680 11.019 12348 Z= 0.350 Chirality : 0.046 0.192 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.855 79.376 1403 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.32 % Allowed : 21.24 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.46 (0.24), residues: 1134 helix: 0.43 (0.25), residues: 394 sheet: -1.25 (0.32), residues: 248 loop : -1.96 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS A 287 PHE 0.014 0.002 PHE A 341 TYR 0.018 0.002 TYR R 212 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.142 Fit side-chains REVERT: A 271 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8518 (tt) REVERT: A 294 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7110 (pm20) REVERT: R 23 TRP cc_start: 0.7287 (p-90) cc_final: 0.6920 (p-90) REVERT: H 11 LEU cc_start: 0.7745 (tp) cc_final: 0.7432 (mp) REVERT: H 18 ARG cc_start: 0.7312 (tpp80) cc_final: 0.7042 (tpt-90) REVERT: H 148 PRO cc_start: 0.8591 (Cg_endo) cc_final: 0.8195 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7267 (mp0) cc_final: 0.7011 (mp0) REVERT: G 21 MET cc_start: 0.8837 (tpp) cc_final: 0.8593 (tpp) REVERT: G 48 ASP cc_start: 0.8468 (t0) cc_final: 0.8234 (t0) outliers start: 21 outliers final: 20 residues processed: 167 average time/residue: 0.2181 time to fit residues: 50.0964 Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS R 382 ASN R 422 ASN H 39 GLN H 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105797 restraints weight = 13470.127| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.26 r_work: 0.3115 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9074 Z= 0.200 Angle : 0.640 11.808 12348 Z= 0.324 Chirality : 0.044 0.219 1424 Planarity : 0.004 0.060 1540 Dihedral : 7.505 87.387 1403 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.54 % Allowed : 21.46 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1134 helix: 0.93 (0.26), residues: 391 sheet: -1.09 (0.32), residues: 247 loop : -1.81 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS A 287 PHE 0.012 0.001 PHE A 339 TYR 0.012 0.001 TYR H 103 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.942 Fit side-chains REVERT: A 221 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 222 ASN cc_start: 0.8010 (t0) cc_final: 0.7520 (p0) REVERT: A 271 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 294 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7076 (pm20) REVERT: R 23 TRP cc_start: 0.7298 (p-90) cc_final: 0.6932 (p-90) REVERT: H 18 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6857 (tpt-90) REVERT: H 148 PRO cc_start: 0.8571 (Cg_endo) cc_final: 0.8245 (Cg_exo) REVERT: H 246 GLU cc_start: 0.7285 (mp0) cc_final: 0.7074 (mp0) REVERT: G 48 ASP cc_start: 0.8411 (t0) cc_final: 0.8182 (t0) outliers start: 23 outliers final: 16 residues processed: 177 average time/residue: 0.2084 time to fit residues: 51.7207 Evaluate side-chains 166 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 9.9990 chunk 107 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS H 183 GLN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103614 restraints weight = 13671.020| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.36 r_work: 0.3077 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9074 Z= 0.348 Angle : 0.708 14.063 12348 Z= 0.357 Chirality : 0.047 0.276 1424 Planarity : 0.004 0.059 1540 Dihedral : 7.538 89.657 1402 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.65 % Allowed : 21.46 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1134 helix: 0.95 (0.26), residues: 391 sheet: -1.07 (0.32), residues: 248 loop : -1.72 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.004 0.001 HIS A 287 PHE 0.015 0.002 PHE A 341 TYR 0.016 0.002 TYR B 105 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.173 Fit side-chains REVERT: A 221 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 222 ASN cc_start: 0.8020 (t0) cc_final: 0.7566 (p0) REVERT: A 271 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (tt) REVERT: R 23 TRP cc_start: 0.7256 (p-90) cc_final: 0.6904 (p-90) REVERT: R 110 GLN cc_start: 0.9174 (tp40) cc_final: 0.8963 (tp40) REVERT: H 18 ARG cc_start: 0.7304 (tpp80) cc_final: 0.7072 (tpt-90) REVERT: H 148 PRO cc_start: 0.8653 (Cg_endo) cc_final: 0.8314 (Cg_exo) REVERT: H 227 TYR cc_start: 0.8394 (m-10) cc_final: 0.8170 (m-10) REVERT: H 246 GLU cc_start: 0.7449 (mp0) cc_final: 0.7196 (mp0) REVERT: B 156 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: G 48 ASP cc_start: 0.8334 (t0) cc_final: 0.8094 (t0) outliers start: 24 outliers final: 19 residues processed: 178 average time/residue: 0.2156 time to fit residues: 53.3386 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS H 183 GLN B 6 GLN B 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105735 restraints weight = 13306.561| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.33 r_work: 0.3120 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9074 Z= 0.182 Angle : 0.657 13.336 12348 Z= 0.329 Chirality : 0.044 0.278 1424 Planarity : 0.004 0.061 1540 Dihedral : 7.216 84.341 1402 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.54 % Allowed : 22.12 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.73 (0.24), residues: 1134 helix: 1.16 (0.26), residues: 392 sheet: -0.94 (0.32), residues: 247 loop : -1.59 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.008 0.001 HIS A 287 PHE 0.012 0.001 PHE A 339 TYR 0.011 0.001 TYR A 235 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.041 Fit side-chains REVERT: A 221 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8238 (tm-30) REVERT: A 222 ASN cc_start: 0.7863 (t0) cc_final: 0.7381 (p0) REVERT: A 271 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 294 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7102 (pm20) REVERT: R 23 TRP cc_start: 0.7246 (p-90) cc_final: 0.6914 (p-90) REVERT: H 18 ARG cc_start: 0.7340 (tpp80) cc_final: 0.7099 (tpt-90) REVERT: H 148 PRO cc_start: 0.8561 (Cg_endo) cc_final: 0.8268 (Cg_exo) REVERT: B 127 LYS cc_start: 0.8951 (mttm) cc_final: 0.8722 (mmtt) REVERT: B 156 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8483 (pt0) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.2092 time to fit residues: 54.4596 Evaluate side-chains 170 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS H 183 GLN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103738 restraints weight = 13461.098| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.32 r_work: 0.3086 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9074 Z= 0.322 Angle : 0.723 18.680 12348 Z= 0.360 Chirality : 0.047 0.265 1424 Planarity : 0.004 0.059 1540 Dihedral : 7.311 81.424 1402 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.43 % Allowed : 23.45 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.78 (0.24), residues: 1134 helix: 1.09 (0.26), residues: 391 sheet: -0.97 (0.32), residues: 248 loop : -1.57 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.002 PHE A 341 TYR 0.014 0.002 TYR G 40 ARG 0.004 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.033 Fit side-chains REVERT: A 221 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 222 ASN cc_start: 0.7913 (t0) cc_final: 0.7456 (p0) REVERT: A 271 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8461 (tt) REVERT: R 23 TRP cc_start: 0.7262 (p-90) cc_final: 0.6903 (p-90) REVERT: R 154 PHE cc_start: 0.8182 (t80) cc_final: 0.7901 (t80) REVERT: H 18 ARG cc_start: 0.7327 (tpp80) cc_final: 0.7094 (tpt-90) outliers start: 22 outliers final: 20 residues processed: 175 average time/residue: 0.2035 time to fit residues: 49.5965 Evaluate side-chains 168 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 404 TYR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS H 183 GLN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104862 restraints weight = 13471.964| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.30 r_work: 0.3105 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9074 Z= 0.216 Angle : 0.701 18.571 12348 Z= 0.348 Chirality : 0.045 0.247 1424 Planarity : 0.004 0.064 1540 Dihedral : 7.056 68.291 1402 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.32 % Allowed : 23.56 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.68 (0.24), residues: 1134 helix: 1.14 (0.26), residues: 391 sheet: -0.90 (0.32), residues: 247 loop : -1.50 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS A 287 PHE 0.013 0.001 PHE R 182 TYR 0.011 0.001 TYR H 103 ARG 0.004 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5078.62 seconds wall clock time: 90 minutes 40.74 seconds (5440.74 seconds total)