Starting phenix.real_space_refine on Wed Mar 12 20:37:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf6_60051/03_2025/8zf6_60051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf6_60051/03_2025/8zf6_60051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zf6_60051/03_2025/8zf6_60051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf6_60051/03_2025/8zf6_60051.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf6_60051/03_2025/8zf6_60051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf6_60051/03_2025/8zf6_60051_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 53 5.16 5 C 5264 2.51 5 N 1438 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8284 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1865 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2484 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 355 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1888 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 254} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 133 Chain: "S" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1692 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 5.34, per 1000 atoms: 0.64 Number of scatterers: 8284 At special positions: 0 Unit cell: (86.92, 124.02, 127.2, 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 53 16.00 O 1529 8.00 N 1438 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 956.1 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.639A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.615A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.606A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.518A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 18 through 47 removed outlier: 4.559A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 4.125A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 121 removed outlier: 4.008A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 125 removed outlier: 3.915A pdb=" N PHE R 125 " --> pdb=" O PRO R 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 122 through 125' Processing helix chain 'R' and resid 129 through 150 removed outlier: 3.774A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.648A pdb=" N GLY R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.708A pdb=" N ALA R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.588A pdb=" N LEU R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 253 removed outlier: 3.538A pdb=" N VAL R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Proline residue: R 231 - end of helix Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 266 through 284 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 287 through 295 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.226A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.732A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.941A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.614A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.581A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.756A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.564A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.614A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.863A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.602A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.388A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 158 through 159 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.579A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.014A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.539A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.635A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1254 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: 2.53 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1338 1.29 - 1.42: 2329 1.42 - 1.56: 4729 1.56 - 1.69: 2 1.69 - 1.82: 73 Bond restraints: 8471 Sorted by residual: bond pdb=" C HIS A 387 " pdb=" O HIS A 387 " ideal model delta sigma weight residual 1.237 1.156 0.081 1.17e-02 7.31e+03 4.75e+01 bond pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 1.523 1.435 0.089 1.30e-02 5.92e+03 4.67e+01 bond pdb=" CA HIS A 387 " pdb=" C HIS A 387 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.30e-02 5.92e+03 4.36e+01 bond pdb=" CA ALA A 39 " pdb=" C ALA A 39 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.28e-02 6.10e+03 4.33e+01 bond pdb=" CA HIS A 387 " pdb=" CB HIS A 387 " ideal model delta sigma weight residual 1.528 1.433 0.096 1.56e-02 4.11e+03 3.77e+01 ... (remaining 8466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11177 1.88 - 3.76: 294 3.76 - 5.63: 57 5.63 - 7.51: 16 7.51 - 9.39: 6 Bond angle restraints: 11550 Sorted by residual: angle pdb=" N GLN S 183 " pdb=" CA GLN S 183 " pdb=" C GLN S 183 " ideal model delta sigma weight residual 110.41 119.80 -9.39 1.23e+00 6.61e-01 5.83e+01 angle pdb=" C SER S 184 " pdb=" N PRO S 185 " pdb=" CA PRO S 185 " ideal model delta sigma weight residual 119.78 125.62 -5.84 1.03e+00 9.43e-01 3.22e+01 angle pdb=" C GLN A 384 " pdb=" CA GLN A 384 " pdb=" CB GLN A 384 " ideal model delta sigma weight residual 110.79 101.75 9.04 1.66e+00 3.63e-01 2.97e+01 angle pdb=" C ILE A 382 " pdb=" CA ILE A 382 " pdb=" CB ILE A 382 " ideal model delta sigma weight residual 112.22 104.81 7.41 1.38e+00 5.25e-01 2.89e+01 angle pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" C ASP R 81 " ideal model delta sigma weight residual 113.28 121.69 -8.41 1.57e+00 4.06e-01 2.87e+01 ... (remaining 11545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 4499 15.47 - 30.95: 351 30.95 - 46.42: 77 46.42 - 61.90: 12 61.90 - 77.37: 7 Dihedral angle restraints: 4946 sinusoidal: 1680 harmonic: 3266 Sorted by residual: dihedral pdb=" C GLN A 384 " pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" CB GLN A 384 " ideal model delta harmonic sigma weight residual -122.60 -110.74 -11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta harmonic sigma weight residual 122.80 134.58 -11.78 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA LEU R 192 " pdb=" C LEU R 192 " pdb=" N LEU R 193 " pdb=" CA LEU R 193 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1225 0.097 - 0.194: 85 0.194 - 0.291: 5 0.291 - 0.388: 4 0.388 - 0.485: 4 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ARG A 385 " pdb=" N ARG A 385 " pdb=" C ARG A 385 " pdb=" CB ARG A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CA ASP R 81 " pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CB ASP R 81 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1320 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 230 " -0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO R 231 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG S 180 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO S 181 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO S 181 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO S 181 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 32 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C LYS A 32 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 32 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 33 " -0.015 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 184 2.68 - 3.23: 7893 3.23 - 3.79: 12926 3.79 - 4.34: 16840 4.34 - 4.90: 28984 Nonbonded interactions: 66827 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.191 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.259 3.120 ... (remaining 66822 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.009 0.096 8471 Z= 0.607 Angle : 0.799 9.388 11550 Z= 0.460 Chirality : 0.058 0.485 1323 Planarity : 0.006 0.091 1483 Dihedral : 12.395 77.369 2840 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.62 % Allowed : 0.87 % Favored : 98.50 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 7.50 % 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: -0.35 (0.25), residues: 1111 helix: 1.01 (0.27), residues: 382 sheet: -0.51 (0.31), residues: 269 loop : -1.05 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.009 0.002 HIS R 276 PHE 0.026 0.002 PHE S 68 TYR 0.020 0.002 TYR A 263 ARG 0.014 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.888 Fit side-chains REVERT: A 14 GLU cc_start: 0.7097 (tt0) cc_final: 0.6860 (tt0) REVERT: A 381 ASP cc_start: 0.8220 (t0) cc_final: 0.7923 (t0) REVERT: A 386 MET cc_start: 0.7395 (ttm) cc_final: 0.7164 (ttm) REVERT: B 33 ILE cc_start: 0.8200 (tt) cc_final: 0.7872 (mt) REVERT: B 177 THR cc_start: 0.8402 (m) cc_final: 0.8124 (p) REVERT: B 188 MET cc_start: 0.8683 (mmm) cc_final: 0.8330 (mmm) REVERT: B 308 LEU cc_start: 0.7854 (mp) cc_final: 0.7515 (mp) REVERT: S 82 GLN cc_start: 0.8551 (tp40) cc_final: 0.8198 (tm-30) REVERT: S 183 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (mp10) outliers start: 5 outliers final: 2 residues processed: 173 average time/residue: 1.0864 time to fit residues: 200.8853 Evaluate side-chains 146 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain S residue 181 PRO Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS R 45 GLN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105006 restraints weight = 12528.618| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.75 r_work: 0.3230 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8471 Z= 0.269 Angle : 0.638 8.701 11550 Z= 0.331 Chirality : 0.044 0.154 1323 Planarity : 0.005 0.061 1483 Dihedral : 5.061 52.647 1225 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.25 % Allowed : 10.61 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.09 (0.25), residues: 1111 helix: 1.60 (0.27), residues: 377 sheet: -0.42 (0.30), residues: 273 loop : -0.88 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS A 41 PHE 0.021 0.002 PHE S 68 TYR 0.019 0.002 TYR S 190 ARG 0.005 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.828 Fit side-chains REVERT: A 33 ASP cc_start: 0.8045 (m-30) cc_final: 0.7763 (m-30) REVERT: A 219 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6930 (tm-30) REVERT: A 381 ASP cc_start: 0.8260 (t0) cc_final: 0.7919 (t70) REVERT: B 188 MET cc_start: 0.8939 (mmm) cc_final: 0.8522 (mmm) REVERT: R 83 TRP cc_start: 0.5274 (t-100) cc_final: 0.4132 (t-100) REVERT: S 82 GLN cc_start: 0.8714 (tp40) cc_final: 0.8435 (mm-40) REVERT: S 180 ARG cc_start: 0.7324 (mtt90) cc_final: 0.7047 (mtt180) outliers start: 18 outliers final: 8 residues processed: 155 average time/residue: 1.2818 time to fit residues: 210.7231 Evaluate side-chains 145 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN S 39 GLN S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098215 restraints weight = 12705.866| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.74 r_work: 0.3171 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8471 Z= 0.413 Angle : 0.687 9.067 11550 Z= 0.353 Chirality : 0.046 0.140 1323 Planarity : 0.005 0.057 1483 Dihedral : 5.318 55.676 1222 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.62 % Allowed : 13.36 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.07 (0.25), residues: 1111 helix: 1.41 (0.26), residues: 386 sheet: -0.49 (0.31), residues: 268 loop : -0.97 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.011 0.002 HIS A 230 PHE 0.021 0.002 PHE R 107 TYR 0.021 0.002 TYR A 263 ARG 0.007 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.866 Fit side-chains REVERT: A 38 ARG cc_start: 0.7519 (mtp-110) cc_final: 0.7305 (mtt90) REVERT: A 40 THR cc_start: 0.8910 (t) cc_final: 0.8503 (m) REVERT: A 381 ASP cc_start: 0.8287 (t0) cc_final: 0.7980 (t70) REVERT: B 33 ILE cc_start: 0.8193 (tt) cc_final: 0.7875 (mt) REVERT: B 188 MET cc_start: 0.8950 (mmm) cc_final: 0.8589 (mmm) REVERT: B 217 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7854 (pmt) REVERT: B 304 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7891 (ttp-170) REVERT: S 5 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (t) outliers start: 29 outliers final: 13 residues processed: 155 average time/residue: 1.2893 time to fit residues: 211.4120 Evaluate side-chains 158 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 103 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 237 ASN B 239 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100881 restraints weight = 12714.729| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.67 r_work: 0.3213 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8471 Z= 0.200 Angle : 0.577 8.522 11550 Z= 0.297 Chirality : 0.042 0.131 1323 Planarity : 0.005 0.053 1483 Dihedral : 4.915 56.711 1222 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.25 % Allowed : 15.98 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.30 (0.25), residues: 1111 helix: 1.92 (0.27), residues: 377 sheet: -0.40 (0.31), residues: 268 loop : -0.83 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.010 0.001 HIS A 230 PHE 0.014 0.001 PHE A 222 TYR 0.021 0.001 TYR R 275 ARG 0.007 0.000 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.909 Fit side-chains REVERT: A 38 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.7219 (mtt90) REVERT: A 381 ASP cc_start: 0.8276 (t0) cc_final: 0.7974 (t70) REVERT: B 17 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7790 (tt0) REVERT: B 33 ILE cc_start: 0.8205 (tt) cc_final: 0.7915 (mt) REVERT: B 188 MET cc_start: 0.8895 (mmm) cc_final: 0.8488 (mmm) REVERT: R 83 TRP cc_start: 0.5353 (t-100) cc_final: 0.4611 (t-100) REVERT: R 276 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7848 (m-70) REVERT: S 5 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8045 (t) REVERT: S 80 PHE cc_start: 0.8659 (m-80) cc_final: 0.8333 (m-80) REVERT: S 183 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7481 (mm-40) outliers start: 26 outliers final: 8 residues processed: 161 average time/residue: 1.2777 time to fit residues: 218.0748 Evaluate side-chains 154 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 276 HIS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 95 optimal weight: 0.0870 chunk 87 optimal weight: 0.0980 chunk 61 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101853 restraints weight = 12565.905| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.72 r_work: 0.3232 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8471 Z= 0.188 Angle : 0.565 8.887 11550 Z= 0.288 Chirality : 0.041 0.131 1323 Planarity : 0.004 0.052 1483 Dihedral : 4.716 56.267 1222 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.75 % Allowed : 17.73 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.50 (0.25), residues: 1111 helix: 2.04 (0.27), residues: 383 sheet: -0.20 (0.32), residues: 267 loop : -0.77 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 222 TYR 0.022 0.001 TYR R 275 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.895 Fit side-chains REVERT: A 38 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.7256 (mtt90) REVERT: A 221 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8296 (tppp) REVERT: A 381 ASP cc_start: 0.8262 (t0) cc_final: 0.7961 (t70) REVERT: B 17 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7882 (tt0) REVERT: B 33 ILE cc_start: 0.8187 (tt) cc_final: 0.7899 (mt) REVERT: B 188 MET cc_start: 0.8870 (mmm) cc_final: 0.8579 (mmm) REVERT: B 258 ASP cc_start: 0.7611 (t70) cc_final: 0.7352 (t0) REVERT: R 83 TRP cc_start: 0.5283 (t-100) cc_final: 0.5074 (t-100) REVERT: S 5 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8070 (t) REVERT: S 80 PHE cc_start: 0.8623 (m-80) cc_final: 0.8290 (m-80) REVERT: S 183 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7346 (mm-40) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 1.2747 time to fit residues: 214.5895 Evaluate side-chains 153 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.0670 chunk 100 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 75 GLN B 220 GLN B 237 ASN B 239 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099711 restraints weight = 12724.066| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.73 r_work: 0.3200 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8471 Z= 0.287 Angle : 0.610 8.552 11550 Z= 0.312 Chirality : 0.043 0.131 1323 Planarity : 0.005 0.052 1483 Dihedral : 4.922 56.186 1222 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.87 % Allowed : 18.48 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1111 helix: 1.95 (0.26), residues: 384 sheet: -0.20 (0.32), residues: 261 loop : -0.83 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.009 0.001 HIS A 230 PHE 0.015 0.002 PHE R 107 TYR 0.022 0.002 TYR B 85 ARG 0.007 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.910 Fit side-chains REVERT: A 38 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7215 (mtt90) REVERT: A 368 ASP cc_start: 0.7455 (m-30) cc_final: 0.7122 (t0) REVERT: A 381 ASP cc_start: 0.8261 (t0) cc_final: 0.7975 (t70) REVERT: B 17 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7866 (tt0) REVERT: B 33 ILE cc_start: 0.8191 (tt) cc_final: 0.7922 (mt) REVERT: B 156 GLN cc_start: 0.8994 (mt0) cc_final: 0.8780 (mt0) REVERT: B 188 MET cc_start: 0.8873 (mmm) cc_final: 0.8483 (mmm) REVERT: B 217 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8296 (pmt) REVERT: R 126 PRO cc_start: 0.7538 (Cg_endo) cc_final: 0.7318 (Cg_exo) REVERT: S 5 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8044 (t) REVERT: S 80 PHE cc_start: 0.8678 (m-80) cc_final: 0.8320 (m-80) REVERT: S 183 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7494 (mm-40) outliers start: 23 outliers final: 10 residues processed: 153 average time/residue: 1.3061 time to fit residues: 211.8231 Evaluate side-chains 152 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100049 restraints weight = 12643.770| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.72 r_work: 0.3204 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8471 Z= 0.262 Angle : 0.595 8.063 11550 Z= 0.303 Chirality : 0.042 0.128 1323 Planarity : 0.004 0.050 1483 Dihedral : 4.921 57.468 1222 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.00 % Allowed : 19.60 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1111 helix: 1.97 (0.26), residues: 384 sheet: -0.23 (0.32), residues: 261 loop : -0.83 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.009 0.001 HIS A 230 PHE 0.015 0.002 PHE R 107 TYR 0.026 0.002 TYR B 85 ARG 0.009 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.826 Fit side-chains REVERT: A 38 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7270 (mtt90) REVERT: A 368 ASP cc_start: 0.7545 (m-30) cc_final: 0.7219 (t0) REVERT: A 381 ASP cc_start: 0.8258 (t0) cc_final: 0.7985 (t70) REVERT: B 17 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7900 (tt0) REVERT: B 33 ILE cc_start: 0.8214 (tt) cc_final: 0.7950 (mt) REVERT: B 156 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8758 (mt0) REVERT: B 188 MET cc_start: 0.8865 (mmm) cc_final: 0.8475 (mmm) REVERT: S 6 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: S 80 PHE cc_start: 0.8668 (m-80) cc_final: 0.8466 (m-80) REVERT: S 180 ARG cc_start: 0.7340 (mtt90) cc_final: 0.6985 (mtt180) REVERT: S 183 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7541 (mm-40) outliers start: 24 outliers final: 13 residues processed: 155 average time/residue: 1.3134 time to fit residues: 215.1299 Evaluate side-chains 157 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100130 restraints weight = 12781.219| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.73 r_work: 0.3204 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8471 Z= 0.249 Angle : 0.595 7.870 11550 Z= 0.303 Chirality : 0.042 0.128 1323 Planarity : 0.005 0.056 1483 Dihedral : 4.925 58.186 1222 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.75 % Allowed : 20.35 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1111 helix: 2.01 (0.26), residues: 384 sheet: -0.23 (0.32), residues: 261 loop : -0.84 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.012 0.001 HIS A 230 PHE 0.014 0.002 PHE R 107 TYR 0.022 0.002 TYR R 275 ARG 0.009 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.831 Fit side-chains REVERT: A 38 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7249 (mtt90) REVERT: A 381 ASP cc_start: 0.8253 (t0) cc_final: 0.7978 (t70) REVERT: B 17 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7908 (tt0) REVERT: B 33 ILE cc_start: 0.8214 (tt) cc_final: 0.7947 (mt) REVERT: B 156 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8741 (mt0) REVERT: B 188 MET cc_start: 0.8829 (mmm) cc_final: 0.8432 (mmm) REVERT: B 219 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7807 (mtt-85) REVERT: S 180 ARG cc_start: 0.7358 (mtt90) cc_final: 0.7002 (mtt180) REVERT: S 183 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7543 (mm-40) outliers start: 22 outliers final: 12 residues processed: 148 average time/residue: 1.6190 time to fit residues: 253.7641 Evaluate side-chains 148 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.0470 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100062 restraints weight = 12858.216| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.74 r_work: 0.3205 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8471 Z= 0.259 Angle : 0.601 7.740 11550 Z= 0.306 Chirality : 0.042 0.142 1323 Planarity : 0.005 0.052 1483 Dihedral : 4.973 59.582 1222 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.00 % Allowed : 20.22 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1111 helix: 2.00 (0.26), residues: 384 sheet: -0.14 (0.32), residues: 264 loop : -0.88 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.012 0.001 HIS A 230 PHE 0.014 0.002 PHE R 107 TYR 0.023 0.002 TYR R 275 ARG 0.010 0.001 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.915 Fit side-chains REVERT: A 38 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7282 (mtt90) REVERT: A 381 ASP cc_start: 0.8250 (t0) cc_final: 0.7978 (t70) REVERT: B 17 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7921 (tt0) REVERT: B 33 ILE cc_start: 0.8211 (tt) cc_final: 0.7946 (mt) REVERT: B 156 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8717 (mt0) REVERT: B 188 MET cc_start: 0.8828 (mmm) cc_final: 0.8439 (mmm) REVERT: B 219 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7789 (mtt-85) REVERT: R 46 VAL cc_start: 0.6934 (t) cc_final: 0.6694 (p) REVERT: S 180 ARG cc_start: 0.7359 (mtt90) cc_final: 0.7015 (mtt180) REVERT: S 183 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7576 (mm-40) outliers start: 24 outliers final: 14 residues processed: 145 average time/residue: 1.4740 time to fit residues: 226.4963 Evaluate side-chains 150 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.0470 chunk 60 optimal weight: 0.0020 chunk 108 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN R 58 ASN R 276 HIS S 39 GLN S 82 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101293 restraints weight = 12727.523| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.73 r_work: 0.3226 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8471 Z= 0.207 Angle : 0.582 7.496 11550 Z= 0.295 Chirality : 0.042 0.153 1323 Planarity : 0.004 0.049 1483 Dihedral : 4.840 58.882 1222 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.75 % Allowed : 20.60 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.54 (0.25), residues: 1111 helix: 2.12 (0.26), residues: 384 sheet: -0.12 (0.32), residues: 264 loop : -0.84 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.012 0.001 HIS A 230 PHE 0.012 0.001 PHE R 107 TYR 0.024 0.001 TYR R 275 ARG 0.009 0.000 ARG R 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.817 Fit side-chains REVERT: A 38 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7254 (mtt90) REVERT: A 381 ASP cc_start: 0.8256 (t0) cc_final: 0.7980 (t70) REVERT: B 17 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7906 (tt0) REVERT: B 33 ILE cc_start: 0.8193 (tt) cc_final: 0.7925 (mt) REVERT: B 137 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7719 (ttm110) REVERT: B 156 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8708 (mt0) REVERT: B 188 MET cc_start: 0.8813 (mmm) cc_final: 0.8536 (mmm) REVERT: B 219 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: R 46 VAL cc_start: 0.6737 (t) cc_final: 0.6496 (p) REVERT: R 83 TRP cc_start: 0.5154 (t-100) cc_final: 0.4741 (t-100) REVERT: S 180 ARG cc_start: 0.7345 (mtt90) cc_final: 0.6990 (mtt180) REVERT: S 183 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7576 (mm-40) outliers start: 22 outliers final: 11 residues processed: 146 average time/residue: 1.4663 time to fit residues: 226.9422 Evaluate side-chains 151 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN R 276 HIS S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099233 restraints weight = 12881.417| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.75 r_work: 0.3193 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8471 Z= 0.304 Angle : 0.627 7.973 11550 Z= 0.319 Chirality : 0.043 0.165 1323 Planarity : 0.005 0.050 1483 Dihedral : 5.035 57.288 1222 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.12 % Allowed : 21.22 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.47 (0.25), residues: 1111 helix: 1.99 (0.26), residues: 384 sheet: -0.04 (0.32), residues: 270 loop : -0.92 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.013 0.001 HIS A 230 PHE 0.015 0.002 PHE R 107 TYR 0.023 0.002 TYR R 275 ARG 0.009 0.001 ARG R 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6383.48 seconds wall clock time: 111 minutes 13.31 seconds (6673.31 seconds total)